Structure of a bacterial microcompartment shell protein bound to a cobalamin cofactor
The EutL shell protein is a key component of the ethanolamine-utilization microcompartment, which serves to compartmentalize ethanolamine degradation in diverse bacteria. The apparent function of this shell protein is to facilitate the selective diffusion of large cofactor molecules between the cytoplasm and the lumen of the microcompartment. While EutL is implicated in molecular-transport phenomena, the details of its function, including the identity of its transport substrate, remain unknown. Here, the 2.1 Å resolution X-ray crystal structure of a EutL shell protein bound to cobalamin (vitamin B12) is presented a...
Source: Acta Crystallographica Section F - November 13, 2014 Category: Biochemistry Authors: Thompson, M.C.Crowley, C.S.Kopstein, J.Bobik, T.A.Yeates, T.O. Tags: bacterial microcompartments EutL shell protein Clostridium perfringens structural communications Source Type: research

Cloning, expression, purification, crystallization and X-ray crystallographic analysis of PhaA from Ralstonia eutropha
Polyhydroxybutyrate (PHB) is a biopolymer that is in the spotlight because of its broad applications in bioplastics, fine chemicals, implant biomaterials and biofuels. PhaA from Ralstonia eutropha (RePhaA) is the first enzyme in the PHB biosynthetic pathway and catalyzes the condensation reaction of two acetyl-CoA molecules to give acetoacetyl-CoA. RePhaA was crystallized using the hanging-drop vapour-diffusion method in the presence of 20% polyethylene glycol monomethyl ether 2K, 0.1 M Tris–HCl pH 8.5 and 0.2 M trimethylamine N-oxide dihydrate at 295 K. X-ray diffraction data were collected to a maximum resolu...
Source: Acta Crystallographica Section F - October 31, 2014 Category: Biochemistry Authors: Kim, E.-J.Kim, K.-J. Tags: PhaA thiolase polyhydroxyalkanoate Ralstonia eutropha crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of the S-adenosylhomocysteine hydrolase (SAHH) from Thermotoga maritima
S-Adenosylhomocysteine hydrolase (SAHH) catalyzes the reversible conversion of S-adenosylhomocysteine into adenosine and homocysteine. The SAHH from Thermotoga maritima (TmSAHH) was expressed in Escherichia coli and the recombinant protein was purified and crystallized. TmSAHH crystals belonging to space group C2, with unit-cell parameters a = 106.3, b = 112.0, c = 164.9 Å, β = 103.5°, were obtained by the sitting-drop vapour-diffusion method and diffracted to 2.85 Å resolution. Initial phase determination by molecular replacement clearly indicated that the crystal contains one homotetramer per asy...
Source: Acta Crystallographica Section F - October 31, 2014 Category: Biochemistry Authors: He, M.Zheng, Y.Huang, C.-H.Qian, G.Xiao, X.Ko, T.-P.Shao, W.Guo, R.-T. Tags: thermostable enzyme S-adenosylhomocysteine hydrolase Thermotoga maritima crystallization communications Source Type: research

Crystallization and preliminary X-ray analysis of the hypothetical deaminase RPB_0146 from Rhodopseudomonas palustris HaA2
RPB_0146, a putative deaminase from Rhodopseudomonas palustris HaA2, was expressed in Escherichia coli BL21 (DE3) cells and purified using a His6 tag by Ni2+-chelating affinity chromatography for X-ray crystallographic analysis. Diffraction-quality crystals were grown by the hanging-drop vapour-diffusion method at 289 K and diffracted to a resolution of 2.44 Å using a wavelength of 1.000 Å at the Photon Factory (KEK), Japan. The crystals belonged to the orthorhombic space group P212121, with unit-cell parameters a = 66.26, b = 123.94, c = 155.95 Å. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - October 31, 2014 Category: Biochemistry Authors: Zhang, G.Yu, D.Yang, G.Dong, H.Zhang, T.Liu, X. Tags: RPB_0146 deaminase Rhodopseudomonas palustris HaA2 crystallization communications Source Type: research

Ovine β-lactoglobulin at atomic resolution
The crystal structure of the triclinic form of the milk protein β-lactoglobulin from sheep (Ovis aries) at 1.1 Å resolution is described together with a comparison of the triclinic structures of the low-pH bovine and high-pH ovine proteins. All three structures are remarkably similar, despite the well known pH-dependent conformational transition described for the bovine and porcine proteins that occurs in solution. The high resolution of the present structure determination has allowed a more accurate description of the protein than has hitherto been possible, but it is still not clear whether flexibility chang...
Source: Acta Crystallographica Section F - October 31, 2014 Category: Biochemistry Authors: Kontopidis, G.Nordle Gilliver, A.Sawyer, L. Tags: ovine β -lactoglobulin Ovis aries structural communications Source Type: research

Structure of an Escherichia coli Hfq:RNA complex at 0.97 Å resolution
In bacteria, small RNAs (sRNAs) silence or activate target genes through base pairing with the mRNA, thereby modulating its translation. A central player in this process is the RNA chaperone Hfq, which facilitates the annealing of sRNAs with their target mRNAs. Hfq has two RNA-binding surfaces that recognize A-rich and U-rich sequences, and is believed to bind an sRNA–mRNA pair simultaneously. However, how Hfq promotes annealing remains unclear. Here, the crystal structure of Escherichia coli Hfq is presented in complex with U6-RNA bound to its proximal binding site at 0.97 Å resolution, revealing the Hfq&nda...
Source: Acta Crystallographica Section F - October 31, 2014 Category: Biochemistry Authors: Schulz, E.C.Barabas, O. Tags: Hfq RNA chaperones Escherichia coli structural communications Source Type: research

Optimization of crystallization conditions for biological macromolecules
For the successful X-ray structure determination of macromolecules, it is first necessary to identify, usually by matrix screening, conditions that yield some sort of crystals. Initial crystals are frequently microcrystals or clusters, and often have unfavorable morphologies or yield poor diffraction intensities. It is therefore generally necessary to improve upon these initial conditions in order to obtain better crystals of sufficient quality for X-ray data collection. Even when the initial samples are suitable, often marginally, refinement of conditions is recommended in order to obtain the highest quality crystals that...
Source: Acta Crystallographica Section F - October 30, 2014 Category: Biochemistry Authors: McPherson, A.Cudney, B. Tags: precipitants pH additives X-ray diffraction proteins strategy crystal growth nucleation crystallization communications Source Type: research

Crystallization, room-temperature X-ray diffraction and preliminary analysis of Kaposi's sarcoma herpesvirus LANA bound to DNA
This report describes the rational protein engineering for successful co-crystallization with DNA and X-ray diffraction data collection at room temperature on the high-brilliance third-generation synchrotron PETRA III at DESY, Germany. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Hellert, J.Krausze, J.Schulz, T.F.Lührs, T. Tags: Kaposi's sarcoma herpesvirus structure-guided mutagenesis latency-associated nuclear antigen laboratory communications Source Type: research

Crystallization and preliminary X-ray diffraction studies of an l-amino-acid oxidase from Lachesis muta venom
Snake-venom proteins form multi-component defence systems by the recruitment and rapid evolution of nonvenomous proteins and hence serve as model systems to understand the structural modifications that result in toxicity. l-Amino-acid oxidases (LAAOs) are encountered in a number of snake venoms and have been implicated in the inhibition of platelet aggregation, cytotoxicity, haemolysis, apoptosis and haemorrhage. An l-amino-acid oxidase from Lachesis muta venom has been purified and crystallized. The crystals belonged to space group P21, with unit-cell parameters a = 66.05, b = 79.41, c = 100.52 Å, β = 96.55&d...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Ullah, A.Masood, R.Spencer, P.J.Murakami, M.T.Arni, R.K. Tags: l-amino-acid oxidase Lachesis muta crystallization communications Source Type: research

Purification, crystallization and preliminary X-ray diffraction analysis of pyridoxal kinase from Plasmodium falciparum (PfPdxK)
Pyridoxal kinases (PdxK) catalyze the phosphorylation of vitamin B6 precursors. Thus, these enzymes are an essential part of many metabolic processes in all organisms. The protozoan parasite Plasmodium falciparum (the main causative agent of Malaria tropica) possesses a unique de novo B6-biosynthesis pathway in addition to a interconversion pathway based on the activity of plasmodial PdxK (PfPdxK). The role of PdxK in B6 salvage has prompted previous authors to suggest PdxK as a promising target for structure-based antimalarial drug design. Here, the expression, purification, crystallization and preliminary X-ray diffracti...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Kronenberger, T.Lunev, S.Wrenger, C.Groves, M.R. Tags: malaria Plasmodium falciparum vitamin B6 biosynthesis and salvage pyridoxal kinase crystallization communications Source Type: research

Use of a novel microtitration protocol to obtain diffraction-quality crystals of 4-hydroxy-2-oxoglutarate aldolase from Bos taurus
The enzyme 4-hydroxy-2-oxoglutarate aldolase (HOGA) catalyses the retro-aldol degradation of 4-hydroxy-2-oxoglutarate to pyruvate and glyoxylate as part of the hydroxyproline catabolic pathway in mammals. Mutations in the coding region of the human HOGA gene are associated with primary hyperoxaluria type 3, a disease characterized by excessive oxalate production and ultimately stone deposition. Native HOGA was purified from bovine kidney using an improved and streamlined purification protocol from which two crystal forms were obtained using two different approaches. Vapour diffusion using PEG 3350 as a precipitant produced...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Huang, A.Baker, E.Loomes, K. Tags: primary hyperoxaluria DHDPSL 4-hydroxy-2-oxoglutarate aldolase Bos taurus crystallization communications Source Type: research

Purification, crystallization and preliminary X-ray crystallographic analysis of the flagellar accessory protein FlaH from the methanogenic archaeon Methanocaldococcus jannaschii
The flagellar accessory protein FlaH is thought to be one of the essential components of an archaeal motility system. However, to date biochemical and structural information about this protein has been limited. Here, the crystallization of FlaH from the hyperthermophilic archaeon Methanocaldococcus jannaschii is reported. Protein crystals were obtained by the vapour-diffusion method. These crystals belonged to space group P3121, with unit-cell parameters a = b = 131.42, c = 89.35 Å. The initial solution of the FlaH structure has been determined by multiple-wavelength anomalous dispersion phasing using a selenomethi...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Meshcheryakov, V.A.Yoon, Y.-H.Matsunami, H.Wolf, M. Tags: FlaH Methanocaldococcus jannaschii crystallization communications Source Type: research

Purification, crystallization and preliminary crystallographic investigation of FrnE, a disulfide oxidoreductase from Deinococcus radiodurans
In prokaryotes, Dsb proteins catalyze the formation of native disulfide bonds through an oxidative folding pathway and are part of the cell machinery that protects proteins from oxidative stress. Deinococcus radiodurans is an extremophile which shows unparalleled resistance to ionizing radiation and oxidative stress. It has a strong mechanism to protect its proteome from oxidative damage. The genome of Deinococcus shows the presence of FrnE, a Dsb protein homologue that potentially provides the bacterium with oxidative stress tolerance. Here, crystallization and preliminary X-ray crystallographic analysis of FrnE from D. r...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Panicker, L.Misra, H.S.Bihani, S.C. Tags: Deinococcus radiodurans FrnE disulfide oxidoreductase oxidative stress Dsb proteins crystallization communications Source Type: research

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of the extracellular olfactomedin domain of gliomedin
Gliomedin (GLDN) is one of the essential proteins in the development of the nodes of Ranvier in the vertebrate peripheral nervous system. An olfactomedin (OLF) domain is located at the GLDN extracellular C-terminus and is involved in the accumulation of neuronal plasma membrane voltage-gated sodium channels in the nodes by interacting with neurofascin and NrCAM. No structures of OLF domains have previously been reported. Here, the crystallization of the rat GLDN OLF domain, which was expressed in an insect-cell system, is reported. The crystal diffracted to 1.55 Å resolution and belonged to space group P21, with un...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Han, H.Kursula, P. Tags: olfactomedin Schwann cell gliomedin myelin cell adhesion crystallization communications Source Type: research

In situ proteolysis, crystallization and preliminary X-ray diffraction analysis of a VHH that binds listeria internalin B
The variable region of camelid heavy-chain antibodies produces the smallest known antibody fragment with antigen-binding capability (a VHH). The VHH R303 binds internalin B (InlB), a virulence factor expressed by the pathogen Listeria monocytogenes. InlB is critical for initiation of Listeria infection, as it binds a receptor (c-Met) on epithelial cells, triggering the entry of bacteria into host cells. InlB is surface-exposed and is required for virulence, hence a VHH targeting InlB has potential applications for pathogen detection or therapeutic intervention. Here, the expression, purification, crystallization and X-ray ...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Huh, I.Gene, R.Kumaran, J.MacKenzie, C.R.Brooks, C.L. Tags: single-domain antibodies VHH nanobodies Listeria monocytogenes virulence factor crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction data of β-galactosidase from Aspergillus niger
β-Galactosidase from Aspergillus niger (An-β-Gal), belonging to the family 35 glycoside hydrolases, hydrolyzes the β-galactosidase linkages in lactose and other galactosides. It is extensively used in industry owing to its high hydrolytic activity and safety. The enzyme has been expressed in yeasts and purified by immobilized metal-ion affinity chromatography for crystallization experiments. The recombinant An-β-Gal, deglycosylated to avoid heterogeneity of the sample, has a molecular mass of 109 kDa. Rod-shaped crystals grew using PEG 3350 as the main precipitant agent. A diffraction data set was col...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Rico-Díaz, A.Vizoso Vázquez, Á.Cerdán, M.E.Becerra, M.Sanz-Aparicio, J. Tags: β -galactosidase glycosidase hydrolase family 35 Aspergillus niger crystallization communications Source Type: research

Purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies of great cormorant (Phalacrocorax carbo) haemoglobin
Haemoglobin is the iron-containing oxygen-transport metalloprotein that is present in the red blood cells of all vertebrates. In recent decades, there has been substantial interest in attempting to understand the structural basis and functional diversity of avian haemoglobins. Towards this end, purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies have been carried out on cormorant (Phalacrocorax carbo) haemoglobin. Crystals were grown by the hanging-drop vapour-diffusion method using PEG 3350, NaCl and glycerol as precipitants. The crystals belonged to the trigonal system P3121, wi...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Jagadeesan, G.Malathy, P.Gunasekaran, K.Harikrishna Etti, S.Aravindhan, S. Tags: avian haemoglobin great cormorant Phalacrocorax carbo molecular replacement crystallization communications Source Type: research

Crystallization and preliminary X-ray crystallographic analysis of an artificial molten-globular-like triosephosphate isomerase protein of mixed phylogenetic origin
In this report, the ccTIM protein was successfully crystallized using the microbatch-under-oil method and a full X-ray diffraction data set was collected to 2.2 Å resolution using a synchrotron-radiation source. The crystals belonged to space group C2221, with unit-cell parameters a = 107.97, b = 187.21, c = 288.22 Å. Matthews coefficient calculations indicated the presence of six dimers in the asymmetric unit, with an approximate solvent content of 46.2%. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Goyal, V.D.Yadav, P.Kumar, A.Ghosh, B.Makde, R.D. Tags: protein engineering triosephosphate isomerase consensus design molten globule crystallization communications Source Type: research

Overproduction, crystallization and preliminary X-ray crystallographic analysis of Escherichia coli tRNA N6-threonylcarbamoyladenosine dehydratase
Escherichia coli tRNA N6-threonylcarbamoyladenosine dehydratase (TcdA), previously called CsdL or YgdL, was overproduced and purified from E. coli and crystallized using polyethylene glycol 3350 as a crystallizing agent. X-ray diffraction data were collected to 2.70 Å resolution under cryoconditions using synchrotron X-rays. The crystals belonged to space group P21, with unit-cell parameters a = 65.4, b = 96.8, c = 83.3 Å, β = 111.7°. According to the Matthews coefficient, the asymmetric unit may contain up to four subunits of the monomeric protein, with a crystal volume per protein mass (VM) of 2....
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Kim, S.Kim, K.Y.Park, J.K.Lee, B.I.Kim, Y.-G.Park, S. Tags: tRNA hypermodification N6-threonylcarbamoyladenosine dehydratase TcdA CsdL crystallization communications Source Type: research

Cloning, expression, purification, crystallization and preliminary X-ray characterization of allantoinase from Bacillus licheniformis ATCC 14580
Allantoinase, a member of the amidohydrolase superfamily, exists in a wide variety of organisms, including bacteria, fungi, plants and a few animals, such as fishes and amphibians. Allantoinase catalyzes the reversible hydrolysis of allantoin into allantoate by hydrolytic cleavage of the N1—C2 amide bond of the five-membered hydantoin ring. Allantoinase from Bacillus licheniformis (AllBali) presents an inverted enantioselectivity towards allantoin (R-enantioselective), which is a distinguishable feature that is not observed for other allantoinases. In this work, B. licheniformis ATCC 14580 allantoinase (AllBali) cont...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Conejero-Muriel, M.Martínez-Gómez, A.I.Martínez-Rodríguez, S.Gavira, J.A. Tags: amidohydrolase allantoinase Bacillus licheniformis crystallization communications Source Type: research

Purification, crystallization and preliminary X-ray diffraction analysis of NADP-dependent glutamate dehydrogenase from Aspergillus niger
In this study, Aspergillus niger NADP-GDH (AnGDH) has been overexpressed and purified. Purified AnGDH, with a high specific activity of 631.1 units per milligram of protein, was crystallized and the crystal diffracted to 2.9 Å resolution using a home X-ray source. Preliminary analysis of the X-ray diffraction data showed that the crystal belonged to space group R32, with unit-cell parameters a = b = 173.8, c = 241.5 Å, α = β = 90, γ = 120°. The crystals exhibited an unusually high solvent content (83.0%) and had only one molecule in the asymmetric unit. Initial phases were obtained by m...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Prakash, P.Walvekar, A.S.Punekar, N.S.Bhaumik, P. Tags: glutamate dehydrogenase Aspergillus niger crystallization communications Source Type: research

Production, crystallization and preliminary X-ray diffraction of the Gαs α-helical domain in complex with a nanobody
GPCR–G-protein complexes are one of the most important components of cell-signalling cascades. Extracellular signals are sensed by membrane-associated G-protein-coupled receptors (GPCRs) and transduced via G proteins towards intracellular effector molecules. Structural studies of these transient complexes are crucial to understand the molecular details of these interactions. Although a nucleotide-free GPCR–G-protein complex is stable, it is not an ideal sample for crystallization owing to the intrinsic mobility of the Gαs α-helical domain (AHD). To stabilize GPCR–G-protein complexes in a nucle...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Triest, S.Wohlkönig, A.Pardon, E.Steyaert, J. Tags: GPCR transmembrane signalling nanobody-enabled X-ray crystallography G protein crystallization communications Source Type: research

Structure of type II dehydroquinase from Pseudomonas aeruginosa
Pseudomonas aeruginosa causes opportunistic infections and is resistant to most antibiotics. Ongoing efforts to generate much-needed new antibiotics include targeting enzymes that are vital for P. aeruginosa but are absent in mammals. One such enzyme, type II dehydroquinase (DHQase), catalyzes the interconversion of 3-dehydroquinate and 3-dehydroshikimate, a necessary step in the shikimate pathway. This step is vital for the proper synthesis of phenylalanine, tryptophan, tyrosine and other aromatic metabolites. The recombinant expression, purification and crystal structure of catalytically active DHQase from P. aeruginosa ...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Reiling, S.Kelleher, A.Matsumoto, M.M.Robinson, G.Asojo, O.A. Tags: type II dehydroquinase Pseudomonas aeruginosa shikimate pathway structural communications Source Type: research

The structure of rice weevil pectin methylesterase
Rice weevils (Sitophilus oryzae) use a pectin methylesterase (EC 3.1.1.11), along with other enzymes, to digest cell walls in cereal grains. The enzyme is a right-handed β-helix protein, but is circularly permuted relative to plant and bacterial pectin methylesterases, as shown by the crystal structure determination reported here. This is the first structure of an animal pectin methylesterase. Diffraction data were collected to 1.8 Å resolution some time ago for this crystal form, but structure solution required the use of molecular-replacement techniques that have been developed and similar structures that ha...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Teller, D.C.Behnke, C.A.Pappan, K.Shen, Z.Reese, J.C.Reeck, G.R.Stenkamp, R.E. Tags: Sitophilus oryzae rice weevil pectin methylesterase structural communications Source Type: research

Structure of the methanofuran/methanopterin-biosynthetic enzyme MJ1099 from Methanocaldococcus jannaschii
Prior studies have indicated that MJ1099 from Methanocaldococcus jannaschii has roles in the biosynthesis of tetrahydromethanopterin and methanofuran, two key cofactors of one-carbon (C1) metabolism in diverse organisms including the methanogenic archaea. Here, the structure of MJ1099 has been solved to 1.7 Å resolution using anomalous scattering methods. The results indicate that MJ1099 is a member of the TIM-barrel superfamily and that it is a homohexamer. Bioinformatic analyses identified a potential active site that is highly conserved among MJ1099 homologs and the key amino acids involved were identified. The ...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Bobik, T.A.Morales, E.J.Shin, A.Cascio, D.Sawaya, M.R.Arbing, M.Yeates, T.O.Rasche, M.E. Tags: methanofuran methanopterin Methanocaldococcus jannaschii MJ1099 structural communications Source Type: research

New crystal structures of adenylate kinase from Streptococcus pneumoniae D39 in two conformations
Adenylate kinases (AdKs; EC 2.7.3.4) play a critical role in intercellular homeostasis by the interconversion of ATP and AMP to two ADP molecules. Crystal structures of adenylate kinase from Streptococcus pneumoniae D39 (SpAdK) have recently been determined using ligand-free and inhibitor-bound crystals belonging to space groups P21 and P1, respectively. Here, new crystal structures of SpAdK in ligand-free and inhibitor-bound states determined at 1.96 and 1.65 Å resolution, respectively, are reported. The new ligand-free crystal belonged to space group C2, with unit-cell parameters a = 73.5, b = 54.3, c = 62.7 &A...
Source: Acta Crystallographica Section F - October 24, 2014 Category: Biochemistry Authors: Thach, T.T.Lee, S. Tags: adenylate kinase Streptococcus pneumoniae ligand-free inhibitor-bound structural communications Source Type: research

Felix Frolow (1947–2014)
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - September 30, 2014 Category: Biochemistry Authors: Livnah, O.Shimon, L. Tags: obituary Felix Frolow obituaries Source Type: research

A drunken search in crystallization space
The REMARK280 field of the Protein Data Bank is the richest open source of successful crystallization information. The REMARK280 field is optional and currently uncurated, so significant effort needs to be applied to extract reliable data. There are well over 15 000 crystallization conditions available commercially from 12 different vendors. After putting the PDB crystallization information and the commercial cocktail data into a consistent format, these data are used to extract information about the overlap between the two sets of crystallization conditions. An estimation is made as to which commercially available condi...
Source: Acta Crystallographica Section F - September 30, 2014 Category: Biochemistry Authors: Fazio, V.J.Peat, T.S.Newman, J. Tags: crystallization crystallization space crystallization communications Source Type: research

Enhancing ubiquitin crystallization through surface-entropy reduction
Ubiquitin has many attributes suitable for a crystallization chaperone, including high stability and ease of expression. However, ubiquitin contains a high surface density of lysine residues and the doctrine of surface-entropy reduction suggests that these lysines will resist participating in packing interactions and thereby impede crystallization. To assess the contributions of these residues to crystallization behavior, each of the seven lysines of ubiquitin was mutated to serine and the corresponding single-site mutant proteins were expressed and purified. The behavior of these seven mutants was then compared with that ...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Loll, P.J.Xu, P.Schmidt, J.T.Melideo, S.L. Tags: ubiquitin surface-entropy reduction laboratory communications Source Type: research

Crystallization and preliminary X-ray diffraction studies of the C-terminal domain of Chlamydia trachomatis CdsD
The inner membrane ring of the bacterial type III secretion system (TTSS) is composed of two proteins. In Chlamydia trachomatis this ring is formed by CdsD (gene name CT_664) and CdsJ (gene name CTA_0609). CdsD consists of 829 amino acids. The last 400 amino acids at its C-terminal end relate it to the type III secretion system YscD/HrpQ protein family. The C-terminal domain, consisting of amino acids 558–771, of C. trachomatis CdsD was overexpressed in Escherichia coli and purified using immobilized metal-affinity chromatography (IMAC) and size-exclusion chromatography. The protein was crystallized using the vapour-...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Meriläinen, G.Wierenga, R.K. Tags: type III secretion system Chlamydia CdsD crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of full-length spr1814, a response regulator of Streptococcus pneumoniae, in complex with a phosphoryl analogue
Spr1814 of Streptococcus pneumoniae is a signal transduction response regulator belonging to the NarL/FixJ subfamily, which has a helix–turn–helix DNA-binding effector domain. To understand how the phosphorylation of the conserved aspartic acid residue induces conformational changes in spr1814 allowing binding to the target promoter, recombinant spr1814 expressed in Escherichia coli was crystallized with the phosphoryl analogue beryllium fluoride BeF3− by the hanging-drop vapour-diffusion method. The crystals diffracted to 1.9 Å resolution and belonged to space group P21, with unit-cell parameters...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Park, A.Oh, J.S.Chi, Y.M.Jeong, S.W. Tags: Streptococcus pneumoniae Spr1814 crystallization communications Source Type: research

Production, crystallization and preliminary crystallographic analysis of Allochromatium vinosum thiosulfate dehydrogenase TsdA, an unusual acidophilic c-type cytochrome
The ability to perform the very simple oxidation of two molecules of thiosulfate to tetrathionate is widespread among prokaryotes. Despite the prevalent occurrence of tetrathionate formation and its well documented significance within the sulfur cycle, little is known about the enzymes that catalyze the oxidative condensation of two thiosulfate anions. To fill this gap, the thiosulfate dehydrogenase (TsdA) enzyme from the purple sulfur bacterium Allochromatium vinosum was recombinantly expressed in Escherichia coli, purified and crystallized, and a crystallographic data set was collected. The crystals belonged to the monoc...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Brito, J.A.Gutierres, A.Denkmann, K.Dahl, C.Archer, M. Tags: thiosulfate dehydrogenase Allochromatium vinosum c-type cytochrome sulfur metabolism crystallization communications Source Type: research

Crystallization and preliminary crystallographic analysis of poly(3-hydroxybutyrate) depolymerase from Bacillus thuringiensis
Poly[(R)-3-hydroxybutyrate] (PHB) is a microbial biopolymer that has been commercialized as biodegradable plastics. The key enzyme for the degradation is PHB depolymerase (PhaZ). A new intracellular PhaZ from Bacillus thuringiensis (BtPhaZ) has been screened for potential applications in polymer biodegradation. Recombinant BtPhaZ was crystallized using 25% polyethylene glycol 3350, 0.2 M ammonium acetate, 0.1 M bis-tris pH 6.5 at 288 K. The crystals belonged to space group P1, with unit-cell parameters a = 42.97, b = 83.23, c = 85.50 Å, α = 73.45, β = 82.83, γ = 83.49°. An X-ray diffracti...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Wang, Y.-L.Lin, Y.-T.Chen, C.-L.Shaw, G.-C.Liaw, S.-H. Tags: poly(3-hydroxybutyrate) depolymerase PhaZ Bacillus thuringiensis crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of a novel sphingomyelinase D from Loxosceles gaucho venom
Brown spider envenomation results in dermonecrosis, intravascular coagulation, haemolysis and renal failure, mainly owing to the action of sphingomyelinases D (SMases D), which catalyze the hydrolysis of sphingomyelin to produce ceramide 1-phosphate and choline or the hydrolysis of lysophosphatidylcholine to produce lysophosphatidic acid. Here, the heterologous expression, purification, crystallization and preliminary X-ray diffraction analysis of LgRec1, a novel SMase D from Loxosceles gaucho venom, are reported. The crystals belonged to space group P21212, with unit-cell parameters a = 52.98, b = 62.27, c = 84.84 &Arin...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Ullah, A.Magalhães, G.S.Masood, R.Mariutti, R.B.Coronado, M.A.Murakami, M.T.Barbaro, K.C.Arni, R.K. Tags: sphingomyelinase D Loxosceles gaucho crystallization communications Source Type: research

Purification, crystallization and preliminary X-ray crystallographic studies of Drep2 CIDE domain
In this study, the Drep2 CIDE domain was purified and crystallized by the hanging-drop vapour-diffusion method. X-ray diffraction data were then collected to a resolution of 2.3 Å. The crystals were found to belong to the orthorhombic space group P212121, with unit-cell parameters a = 50.28, b = 88.70, c = 113.37 Å. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Lee, S.M.Park, H.H. Tags: apoptosis DNA fragmentation factor CIDE domain Drep2 Drosophila melanogaster crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of cyclolavandulyl diphosphate synthase, a new member of the cis-isoprenyl diphosphate synthase superfamily
Cyclolavandulyl diphosphate synthase (CLDS; estimated molecular weight 23.1 kDa) from the soil bacterium Streptomyces sp. CL190 is an enzyme that catalyzes both the condensation of two molecules of C5 dimethylallyl diphosphate (DMAPP) and the subsequent cyclization. CLDS was crystallized in the absence and the presence of the substrate DMAPP. Diffraction data were collected at a synchrotron source and the crystals diffracted to 2.00 and 1.73 Å resolution, respectively. The crystal obtained in the absence of DMAPP belonged to space group P212121, with unit-cell parameters a = 39.0, b = 87.5, c = 113.6 Å. T...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Tomita, T.Ozaki, T.Matsuda, K.Nishiyama, M.Kuzuyama, T. Tags: condensing enzyme cyclase cyclolavandulyl diphosphate synthase Streptomyces sp. CL190 terpene crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analyses of the redox-controlled complex of terminal oxygenase and ferredoxin components in the Rieske nonhaem iron oxygenase carbazole 1,9a-dioxygenase
The initial reaction in bacterial carbazole degradation is catalyzed by carbazole 1,9a-dioxygenase, which consists of terminal oxygenase (Oxy), ferredoxin (Fd) and ferredoxin reductase components. The electron-transfer complex between reduced Oxy and oxidized Fd was crystallized at 293 K using the hanging-drop vapour-diffusion method with PEG 3350 as the precipitant under anaerobic conditions. The crystal diffracted to a maximum resolution of 2.25 Å and belonged to space group P21, with unit-cell parameters a = 97.3, b = 81.6, c = 116.2 Å, α = γ = 90, β = 100.1°. The VM value is 2.85...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Matsuzawa, J.Aikawa, H.Umeda, T.Ashikawa, Y.Suzuki-Minakuchi, C.Kawano, Y.Fujimoto, Z.Okada, K.Yamane, H.Nojiri, H. Tags: Rieske nonhaem iron oxygenase electron-transfer complex terminal oxygenase ferredoxin carbazole 1,9a-dioxygenase crystallization communications Source Type: research

Expression, crystallization and preliminary X-ray analysis of McbB, a multifunctional enzyme involved in β-carboline skeleton biosynthesis
β-Carboline alkaloids (βCs), with tricyclic pyrido[3,4-b]indole rings, have important pharmacological and therapeutic value. In the biosynthesis of βCs, the Pictet–Spengler (PS) cyclization reaction is responsible for the formation of ring structures. McbB is one of a few enzymes that are known to catalyse PS cyclization. It can also catalyse decarboxylation and oxidation. Here, the expression, crystallization and preliminary data analysis of McbB are reported. The crystals diffracted to 2.10 Å resolution and belonged to the monoclinic space group P21, with unit-cell parameters a = 66.06, b = 8...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Wang, H.Zhang, H.Mi, Y.Ju, J.Chen, Q.Zhang, H. Tags: β -carboline alkaloids Pictet – Spengler cyclization McbB Marinactinospora thermotolerans crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of Lin1840, a putative β-glucosidase from Listeria innocua
Lin1840 is a putative β-glucosidase that is predicted to be involved in 1,2-β-glucan metabolism since the lin1839 gene encoding a 1,2-β-oligoglucan phosphorylase and the lin1840 gene are located in the same gene cluster. Here, Lin1840 was crystallized. The crystals of Lin1840 diffracted to beyond 1.8 Å resolution. The crystal belonged to space group I121, with unit-cell parameters a = 89.75, b = 95.10, c = 215.00 Å, α = 90.00, β = 96.34, γ = 90.00°. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Nakajima, M.Yoshida, R.Miyanaga, A.Taguchi, H. Tags: β -glucosidase 1,2- -glucan crystallization communications Source Type: research

Cloning, expression, purification and preliminary X-ray analysis of EstN2, a novel archaeal α/β-hydrolase from Candidatus Nitrososphaera gargensis
EstN2 is a novel α/β-hydrolase originating from the ammonia-oxidizing thaumarchaeon Candidatus Nitrososphaera gargensis. The genome of the organism was sequenced and genes conferring putative lipolytic activity were amplified and cloned into Escherichia coli as a heterologous host. Through function-based screening, esterase and lipase activity was detected. A recombinant enzyme designated EstN2 was successfully expressed, purified and crystallized. The crystals belonged to space group I2, with one molecule per asymmetric unit, and diffracted X-rays to 1.5 Å resolution. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Kaljunen, H.Chow, J.Streit, W.R.Mueller-Dieckmann, J. Tags: EstN2 α / β -hydrolase Candidatus Nitrososphaera gargensis crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of the BRPF1 bromodomain in complex with its H2AK5ac and H4K12ac histone-peptide ligands
The bromodomain-PHD finger protein 1 (BRPF1) is an essential subunit of the monocytic leukemia zinc (MOZ) histone acetyltransferase (HAT) complex and is required for complex formation and enzymatic activation. BRPF1 contains a structurally conserved bromodomain, which recognizes specific acetyllysine residues on histone proteins. The MOZ HAT plays a direct role in hematopoiesis, and deregulation of its activity is linked to the development of acute myeloid leukemia. However, the molecular mechanism of histone-ligand recognition by the BRPF1 bromodomain is currently unknown. The 117-amino-acid BRPF1 bromodomain was overexpr...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Lubula, M.Y.Poplawaski, A.Glass, K.C. Tags: BRPF1 bromodomain H4K12ac H2AK5ac crystallization communications Source Type: research

Crystallization and preliminary X-ray crystallographic studies of CrArsM, an arsenic(III) S-adenosylmethionine methyltransferase from Chlamydomonas reinhardtii
Arsenic is one the most toxic environmental substances. Arsenic is ubiquitous in water, soil and food, and ranks first on the Environmental Protection Agency's Superfund Priority List of Hazardous Substances. Arsenic(III) S-adenosylmethionine methyltransferases (AS3MT in animals and ArsM in microbes) are key enzymes of arsenic biotransformation, catalyzing the methylation of inorganic arsenite to give methyl, dimethyl and trimethyl products. Arsenic methyltransferases are found in members of every kingdom from bacteria to humans (EC 2.1.1.137). In the human liver, hAS3MT converts inorganic arsenic into more toxic and carci...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Packianathan, C.Pillai, J.K.Riaz, A.Kandavelu, P.Sankaran, B.Rosen, B.P. Tags: S-adenosylmethionine methyltransferase Chlamydomonas reinhardtii crystallization communications Source Type: research

Crystallization of the Ets1–Runx1–CBFβ–DNA complex formed on the TCRα gene enhancer
Gene transcription is regulated in part through the assembly of multiple transcription factors (TFs) on gene enhancers. To enable examination of the mechanism underlying the formation of these complexes and their response to a phosphorylation signal, two kinds of higher-order TF–DNA assemblies were crystallized composed of an unmodified or phosphorylated Ets1 fragment, a Runx1(L94K) fragment and a CBFβ fragment on the T-cell receptor (TCR) α gene enhancer. Within these complexes, the Ets1 and Runx1 fragments contain intrinsically disordered regulatory regions as well as their DNA-binding domains. Crystals ...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Shiina, M.Hamada, K.Inoue-Bungo, T.Shimamura, M.Baba, S.Sato, K.Ogata, K. Tags: Runx1 Ets1 CBF β TCR gene enhancer chemical modification transcription crystallization communications Source Type: research

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of fructose-1,6-bisphosphate aldolase from Escherichia coli
Fructose-1,6-bisphosphate aldolase is one of the most important enzymes in the glycolytic pathway and catalyzes the reversible cleavage of fructose-1,6-bisphosphate to dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. The full-length fbaB gene encoding fructose-1,6-bisphosphate aldolase class I (FBPA I) was cloned from Escherichia coli strain BL21. FBPA I was overexpressed in E. coli and purified. Biochemical analysis found that the optimum reaction temperature of FBPA I is 330.5 K and that the enzyme has a high temperature tolerance. Crystals of recombinant FBPA I were obtained by the sitting-drop vapour-diffus...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Zhang, L.Guo, Z.Huang, J.Liu, M.Wang, Y.Ji, C. Tags: thermostability Ec-FBPA I fructose-1,6-bisphosphate aldolase crystallization communications Source Type: research

Purification and X-ray crystallographic analysis of 7-keto-8-aminopelargonic acid (KAPA) synthase from Mycobacterium smegmatis
7-Keto-8-aminopelargonic acid synthase (KAPA synthase; BioF) is an essential enzyme for mycobacterial growth that catalyses the first committed step in the biotin-synthesis pathway. It is a pyridoxal 5′-phosphate (PLP)-dependent enzyme and is a potential drug target. Here, the cloning, expression, purification and crystallization of KAPA synthase from Mycobacterium smegmatis (MsBioF) and the characterization of MsBioF crystals using X-ray diffraction are described. The crystals diffracted to 2.3 Å resolution and belonged to the monoclinic space group P21, with unit-cell parameters a = 70.88, b = 91.68, c = 10...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Fan, S.Li, D.Fleming, J.Hong, Y.Chen, T.Zhou, L.Bi, L.Wang, D.Zhang, X.Chen, G. Tags: Mycobacterium smegmatis biotin-synthesis pathway 7-keto-8-aminopelargonic acid (KAPA) synthase crystallization communications Source Type: research

Expression, crystallization and preliminary X-ray crystallographic analysis of cystathionine β-lyase from Acinetobacter baumannii OXA-23
Multidrug-resistant Acinetobacter baumannii (Ab) has emerged as a leading nosocomial pathogen because of its resistance to most currently available antibiotics. Cystathionine β-lyase (CBL), a pyridoxal 5′-phosphate (PLP)-dependent enzyme, catalyzes the second step in the transsulfuration pathway, which is essential for the metabolic interconversion of the sulfur-containing amino acids homocysteine and methionine. The enzymes of the transsulfuration pathway are considered to be attractive drug targets owing to their specificity to microbes and plants. As a potential target for the development of novel antibacteri...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Nguyen, D.-Q.Ngo, H.-P.-T.Ahn, Y.-J.Lee, S.H.Kang, L.-W. Tags: cystathionine β -lyase PLP-dependent enzyme multidrug-resistant Acinetobacter baumannii crystallization communications Source Type: research

Cloning, expression, purification, crystallization and preliminary X-ray diffraction of a lysine-specific permease from Pseudomonas aeruginosa
The prokaryotic lysine-specific permease (LysP) belongs to the amino acid–polyamine–organocation (APC) transporter superfamily. In the cell, members of this family are responsible for the uptake and recycling of nutrients, for the maintenance of a constant internal ion concentration and for cell volume regulation. The detailed mechanism of substrate selectivity and transport of l-lysine by LysP is not understood. A high-resolution crystal structure would enormously facilitate such an understanding. To this end, LysP from Pseudomonas aeruginosa was recombinantly expressed in Escherichia coli and purified to near...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Nji, E.Li, D.Doyle, D.A.Caffrey, M. Tags: APC transporter superfamily GFP fusion LysP membrane protein crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of the Pax9 paired domain bound to a DC5 enhancer DNA element
Pax genes belong to a family of metazoan transcription factors that are known to play a critical role in eye, ear, kidney and neural development. The mammalian Pax family of transcription factors is characterized by a ∼128-amino-acid DNA-binding paired domain that makes sequence-specific contacts with DNA. The diversity in Pax gene activities emerges from complex modes of interaction with enhancer regions and heterodimerization with multiple interaction partners. Based on in vitro optimal binding-site selection studies and enhancer identification assays, it has been suggested that Pax proteins may recognize and bind th...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Narasimhan, K.Hilbig, A.Udayasuryan, B.Jayabal, S.Kolatkar, P.R.Jauch, R. Tags: δ -crystallin DC5 enhancer Pax9 paired domain crystallization communications Source Type: research

Purification, crystallization and preliminary X-ray crystallographic analysis of human IL-18 and its extracellular complexes
Interleukin-18 (IL-18), a pro-inflammatory cytokine belonging to the interleukin-1 (IL-1) family, is involved in the pathogenesis of autoimmune/autoinflammatory and allergic diseases such as juvenile idiopathic arthritis and bronchial asthma. IL-18 forms a signalling complex with the IL-18 receptor α (IL-18Rα) and β (IL-18Rβ) chains; however, the detailed activation mechanism remains unclear. Here, the IL-18–IL-18Rα binary and IL-18–IL-18Rα–IL-18Rβ ternary complexes were purified and crystallized as well as IL-18 alone. An X-ray diffraction data set for IL-18 was col...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Kimura, T.Tsutsumi, N.Arita, K.Ariyoshi, M.Ohnishi, H.Kondo, N.Shirakawa, M.Kato, Z.Tochio, H. Tags: interleukin-18 IL-1 superfamily interleukin-18 receptor α β immunity inflammation autoimmunity allergy crystallization communications Source Type: research

Expression, purification and preliminary crystallographic analysis of the cryptic polo-box domain of Caenorhabditis elegans ZYG-1
ZYG-1 is a polo-like kinase essential for centriole assembly in Caenorhabditis elegans. The targeting of ZYG-1 to nascent centrioles is via its central cryptic polo-box (CPB) domain. To shed light on the molecular basis of ZYG-1 recruitment, it is necessary to obtain structural knowledge of the ZYG-1 CPB. Here, the expression, purification and preliminary crystallographic analysis of the ZYG-1 CPB are reported. The protein was overexpressed in Escherichia coli strain BL21 (DE3), purified by multi-step chromatography and crystallized using the vapour-diffusion method. Crystals of the wild-type protein exhibited an order&nda...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Shimanovskaya, E.Dong, G. Tags: centriole cryptic polo-box domain Plk4 polo-like kinase ZYG-1 crystallization communications Source Type: research