Crystal and solution structure of the human RIG-I SF2 domain
RIG-I is a pathogen-recognition receptor that recognizes viral 5′-triphosphates carrying double-stranded RNA. Upon binding to these microbe-associated molecular patterns (MAMPs), RIG-I forms oligomers and promotes downstream processes that result in type I interferon production and induction of an antiviral state. Here, the crystal structure of the human RIG-I superfamily 2 ATPase domain crystallized in an unusually elongated and open conformation is reported. The elongated structure is probably induced in part by crystal packing, but nevertheless indicates that the domain is intrinsically very flexible. This flexibi...
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Deimling, T.Cui, S.Lammens, K.Hopfner, K.-P.Witte, G. Tags: RIG-I SF2 helicase structural communications Source Type: research

The RpfC (Rv1884) atomic structure shows high structural conservation within the resuscitation-promoting factor catalytic domain
The first structure of the catalytic domain of RpfC (Rv1884), one of the resuscitation-promoting factors (RPFs) from Mycobacterium tuberculosis, is reported. The structure was solved using molecular replacement once the space group had been correctly identified as twinned P21 rather than the apparent C2221 by searching for anomalous scattering sites in P1. The structure displays a very high degree of structural conservation with the previously published structures of the catalytic domains of RpfB (Rv1009) and RpfE (Rv2450). This structural conservation highlights the importance of the versatile domain composition of the RP...
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Chauviac, F.-X.Robertson, G.Quay, D.H.X.Bagnéris, C.Dumas, C.Henderson, B.Ward, J.Keep, N.H.Cohen-Gonsaud, M. Tags: resuscitation-promoting factor peptidoglycan Mycobacterium tuberculosis structural communications Source Type: research

Structures of a human blood group glycosyltransferase in complex with a photo-activatable UDP-Gal derivative reveal two different binding conformations
Glycosyltransferases (GTs) catalyse the sequential addition of monosaccharides to specific acceptor molecules and play major roles in key biological processes. GTs are classified into two main families depending on the inverted or retained stereochemistry of the glycosidic bond formed during the reaction. While the mechanism of inverting enzymes is well characterized, the precise nature of retaining GTs is still a matter of much debate. In an attempt to clarify this issue, studies were initiated to identify reaction-intermediate states by using a crystallographic approach based on caged substrates. In this paper, two disti...
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Jørgensen, R.Batot, G.Mannerstedt, K.Imberty, A.Breton, C.Hindsgaul, O.Royant, A.Palcic, M.M. Tags: glycosyltransferases photo-activatable substrate UDP-Gal derivative structural communications Source Type: research

Structure of Saccharomyces cerevisiae mitochondrial Qri7 in complex with AMP
In this study, the crystal structure of Qri7 complexed with AMP (a part of TCA) has been determined at 2.94 Å resolution in a new crystal form. The manner of AMP recognition is similar, with some minor variations, among the Qri7/Kae1/YgjD family proteins. The previously reported dimer formation was also observed in this new crystal form. Furthermore, a comparison with the structure of TobZ, which catalyzes a similar reaction to t6A biosynthesis, revealed the presence of a flexible loop that may be involved in tRNA binding. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - July 22, 2014 Category: Biochemistry Authors: Tominaga, T.Kobayashi, K.Ishii, R.Ishitani, R.Nureki, O. Tags: tRNA modification Qri7 AMP Kae1 YgjD TobZ structural communications Source Type: research

Crystallization screening: the influence of history on current practice
While crystallization historically predates crystallography, it is a critical step for the crystallographic process. The rich history of crystallization and how that history influences current practices is described. The tremendous impact of crystallization screens on the field is discussed. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - June 26, 2014 Category: Biochemistry Authors: Luft, J.R.Newman, J.Snell, E.H. Tags: crystallization screening crystallization communications Source Type: research

Preliminary X-ray diffraction analysis of a thermophilic β -1,3 – 1,4-glucanase from Clostridium thermocellum
β -1,3 – 1,4-Glucanases catalyze the specific hydrolysis of internal β -1,4-glycosidic bonds adjacent to the 3-O-substituted glucose residues in mixed-linked β -glucans. The thermophilic glycoside hydrolase CtGlu16A from Clostridium thermocellum exhibits superior thermal profiles, high specific activity and broad pH adaptability. Here, the catalytic domain of CtGlu16A was expressed in Escherichia coli, purified and crystallized in the trigonal space group P3121, with unit-cell parameters a = b = 74.5, c = 182.9   Å , by the sitting-drop vapour-diffusion method and diffracted to 1.95   Å...
Source: Acta Crystallographica Section F - June 19, 2014 Category: Biochemistry Authors: Zhang, L. Zhao, P. Chen, C.-C. Huang, C.-H. Ko, T.-P. Zheng, Y. Guo, R.-T. Tags: glucanase Clostridium thermocellum industrial enzyme crystallization communications Source Type: research

Crystallization and preliminary analysis of the NqrA and NqrC subunits of the Na+-translocating NADH:ubiquinone oxidoreductase from Vibrio cholerae
The Na+-translocating NADH:ubiquinone oxidoreductase (Na+-NQR) from Vibrio cholerae is a membrane protein complex consisting of six different subunits NqrA–NqrF. The major domains of the NqrA and NqrC subunits were heterologously expressed in Escherichia coli and crystallized. The structure of NqrA1–377 was solved in space groups C2221 and P21 by SAD phasing and molecular replacement at 1.9 and 2.1 Å resolution, respectively. NqrC devoid of the transmembrane helix was co-expressed with ApbE to insert the flavin mononucleotide group covalently attached to Thr225. The structure was determined by molecular...
Source: Acta Crystallographica Section F - June 19, 2014 Category: Biochemistry Authors: Vohl, G.Nedielkov, R.Claussen, B.Casutt, M.S.Vorburger, T.Diederichs, K.Möller, H.M.Steuber, J.Fritz, G. Tags: Vibrio cholerae Na -translocating NQR covalently bound FMN crystallization communications Source Type: research

Purification, crystallization and preliminary X-ray analysis of a putative nucleotide phosphohydrolase, YpgQ, from Bacillus subtilis
The histidine-aspartate (HD) domain exerts phosphohydrolase activity on nucleotides and functions in nucleotide metabolism. Sequence analysis suggested that YpgQ from Bacillus subtilis contains the HD domain, but the structure and function of YpgQ remain to be revealed. The recombinant YpgQ protein was overexpressed in an Escherichia coli cell expression system and was purified to homogeneity by Ni–NTA affinity and anion-exchange chromatography. Crystals in space group P21 were obtained in PEG 600 solutions and diffracted X-rays to 2.3 Å resolution. Moreover, X-ray fluorescence scans on YpgQ crystals demonstr...
Source: Acta Crystallographica Section F - June 19, 2014 Category: Biochemistry Authors: Jeon, Y.J.Song, W.S.Yoon, S.I. Tags: YpgQ Bacillus subtilis HD domain phosphohydrolase crystallization communications Source Type: research

Purification, crystallization and room-temperature X-ray diffraction of inositol dehydrogenase LcIDH2 from Lactobacillus casei BL23
Lactobacillus casei BL23 contains two genes, iolG1 and iolG2, homologous with inositol dehydrogenase encoding genes from many bacteria. Inositol dehydrogenase catalyzes the oxidation of inositol with concomitant reduction of NAD+. The protein encoded by iolG2, LcIDH2, has been purified to homogeneity, crystallized and cryoprotected for diffraction at 77 K. The crystals had a high mosaicity and poor processing statistics. Subsequent diffraction measurements were performed without cryoprotectant at room temperature. These crystals were radiation-resistant and a full diffraction data set was collected at room temperature to...
Source: Acta Crystallographica Section F - June 19, 2014 Category: Biochemistry Authors: Bertwistle, D.Vogt, L.Aamudalapalli, H.B.Palmer, D.R.J.Sanders, D.A.R. Tags: inositol dehydrogenase Lactobacillus casei BL23 crystallization communications Source Type: research

Purification, crystallization and preliminary X-ray crystallographic analysis of the UDP-N-acetylmuramoyl-tripeptide-d-alanyl-d-alanine ligase (MurF) from Acinetobacter baumannii
The emergence and global spread of multidrug-resistant Acinetobacter baumannii strains are major threats to public health. Inhibition of peptidoglycan biosynthesis is an effective strategy for the development of antibiotics. The ATP-dependent UDP-N-acetylmuramoyl-tripeptide-d-alanyl-d-alanine ligase (MurF) that is responsible for the last step of peptidoglycan biosynthesis is a validated target for the development of antibiotics. Crystals of A. baumannii MurF in complex with ATP were grown by the microbatch crystallization method at 295 K. The crystals belonged to space group P3221, with unit-cell parameters a = b = 85.4...
Source: Acta Crystallographica Section F - June 19, 2014 Category: Biochemistry Authors: An, Y.J.Jeong, C.-S.Yu, J.H.Chung, K.M.Cha, S.-S. Tags: Acinetobacter baumannii MurF crystallization communications Source Type: research

Crystallization of the carboxy-terminal region of the bacteriophage T4 proximal long tail fibre protein gp34
The phage-proximal part of the long tail fibres of bacteriophage T4 consists of a trimer of the 1289 amino-acid gene product 34 (gp34). Different carboxy-terminal parts of gp34 have been produced and crystallized. Crystals of gp34(726–1289) diffracting X-rays to 2.9 Å resolution, crystals of gp34(781–1289) diffracting to 1.9 Å resolution and crystals of gp34(894–1289) diffracting to 3.0 and 2.0 Å resolution and belonging to different crystal forms were obtained. Native data were collected for gp34(726–1289) and gp34(894–1289), while single-wavelength anomalous diffracti...
Source: Acta Crystallographica Section F - June 19, 2014 Category: Biochemistry Authors: Granell, M.Namura, M.Alvira, S.Garcia-Doval, C.Singh, A.K.Gutsche, I.van Raaij, M.J.Kanamaru, S. Tags: bacteriophage T4 gene product 34 (gp34) crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of Gos1p, a yeast SNARE protein
The Gos1 protein (Golgi SNAP receptor complex member 1) is involved in the SNARE complex, which is the core machinery that drives membrane fusion between cargo-carrying vesicles and their target membranes in the secretory and endocytic pathways in yeast. Truncated versions of the Gos1 protein from Saccharomyces cerevisiae were cloned, expressed, purified and crystallized. The crystal belonged to space group P212121, with unit-cell parameters a = 39.67, b = 43.58, c = 81.94 Å, α = β = γ = 90°. An X-ray diffraction data set was collected at 100 K to 1.63 Å resolution. Matthews coefficie...
Source: Acta Crystallographica Section F - June 19, 2014 Category: Biochemistry Authors: Cheng, B.Zhang, Y.Guo, G.Gao, Y. Tags: Gos1 protein SNARE complex membrane fusion Saccharomyces cerevisiae crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of Xyn30D from Paenibacillus barcinonensis
This study will contribute to the understanding of the role that the different xylanases play in the depolymerization of glucuronoxylan. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - June 19, 2014 Category: Biochemistry Authors: Sainz-Polo, M.Á.Valenzuela, S.V.Pastor, F.J.Sanz-Aparicio, J. Tags: xylanase GH30 CBM35 Paenibacillus barcinonensis crystallization communications Source Type: research

Cloning, overexpression, purification and preliminary X-ray analysis of the protein kinase domain of enhanced disease resistance 1 (EDR1) from Arabidopsis thaliana
Enhanced disease resistance 1 is a member of the Raf-like mitogen-activated protein kinase kinase kinase (MAPKKK) family that negatively regulates disease resistance, ethylene-induced senescence and programmed cell death in response to both abiotic and biotic stresses. A catalytically inactive form of the EDR1 kinase domain was successfully cloned, expressed, purified and crystallized. Crystallization was conducted in the presence of the ATP analogue AMP-PNP. The crystals belonged to space group P3221 and contained two molecules in the asymmetric unit. The crystals diffracted X-rays to 2.55 Å resolution. (Source: A...
Source: Acta Crystallographica Section F - June 19, 2014 Category: Biochemistry Authors: Kaljunen, H.Panneerselvam, S.Mueller-Dieckmann, J. Tags: enhanced disease resistance 1 Arabidopsis thaliana MAPKKK family crystallization communications Source Type: research

Cloning, expression, purification, crystallization and X-ray crystallographic analysis of the (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 from Ralstonia eutropha H16
The (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 from Ralstonia eutropha (RePaaH1) is an enzyme used in the biosynthesis of n-butanol from acetyl-CoA by the reduction of acetoacetyl-CoA to (S)-3-hydroxybutyryl-CoA. The RePaaH1 protein was crystallized using the hanging-drop vapour-diffusion method in the presence of 1.4 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.0, 0.2 M sodium chloride at 295 K. X-ray diffraction data were collected to a maximum resolution of 2.6 Å on a synchrotron beamline. The crystal belonged to space group P3221, with unit-cell parameters a = b = 135.4, c = 97.2 Å. With t...
Source: Acta Crystallographica Section F - June 19, 2014 Category: Biochemistry Authors: Kim, J.Kim, K.-J. Tags: (S)-3-hydroxybutyryl-CoA dehydrogenase Ralstonia eutropha n-butanol crystallization communications Source Type: research

Crystallization and preliminary X-ray crystallographic analysis of the C-terminal domain of guanylate kinase-associated protein from Rattus norvegicus
In this study, the C-terminal helical domain of GKAP from Rattus norvegicus was purified and crystallized by the vapour-diffusion method. To improve the diffraction quality of the GKAP crystals, a flexible loop in GKAP was truncated and an MBP (maltose-binding protein)-GKAP fusion was constructed in which the last C-terminal helix of MBP is fused to the N-terminus of the GKAP domain. The MBP-GKAP crystals diffracted to 2.0 Å resolution using synchrotron radiation. The crystal was orthorhombic, belonging to space group P21212, with unit-cell parameters a = 99.1, b = 158.7, c = 65.5 Å. The Matthews coefficien...
Source: Acta Crystallographica Section F - June 19, 2014 Category: Biochemistry Authors: Tong, J.Yang, H.Im, Y.J. Tags: GKAP scaffolding protein Rattus norvegicus maltose-binding protein crystallization communications Source Type: research

Preliminary X-ray diffraction analysis of a thermophilic β-1,3–1,4-glucanase from Clostridium thermocellum
β-1,3–1,4-Glucanases catalyze the specific hydrolysis of internal β-1,4-glycosidic bonds adjacent to the 3-O-substituted glucose residues in mixed-linked β-glucans. The thermophilic glycoside hydrolase CtGlu16A from Clostridium thermocellum exhibits superior thermal profiles, high specific activity and broad pH adaptability. Here, the catalytic domain of CtGlu16A was expressed in Escherichia coli, purified and crystallized in the trigonal space group P3121, with unit-cell parameters a = b = 74.5, c = 182.9 Å, by the sitting-drop vapour-diffusion method and diffracted to 1.95 Å resolutio...
Source: Acta Crystallographica Section F - June 19, 2014 Category: Biochemistry Authors: Zhang, L.Zhao, P.Chen, C.-C.Huang, C.-H.Ko, T.-P.Zheng, Y.Guo, R.-T. Tags: glucanase Clostridium thermocellum industrial enzyme crystallization communications Source Type: research

Crystallization and preliminary crystallographic analysis of histamine dehydrogenase from Natrinema gari BCC 24369
Histamine dehydrogenase (HADH) catalyzes the oxidative deamination of histamine, resulting in the production of imidazole acetaldehyde and an ammonium ion. The enzyme isolated from the newly identified halophilic archaeon Natrinema gari BCC 24369 is significantly different from the previously described protein from Nocardioides simplex. This newly identified HADH comprises three subunits with molecular weights of 49.0, 24.7 and 23.9 kDa, respectively, and is optimally active under high-salt conditions (3.5–5 M NaCl). As a step in the exploration of the unique properties of the protein, the HADH heterotrimer was p...
Source: Acta Crystallographica Section F - June 19, 2014 Category: Biochemistry Authors: Zhou, D.Visessanguan, W.Chaikaew, S.Benjakul, S.Oda, K.Wlodawer, A. Tags: Natrinema gari BCC 24369 histamine dehydrogenase crystallization communications Source Type: research

Structure of d(CCCCGGTACCGGGG)2 at 1.65   Å resolution
The crystal structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 has previously been reported as an A-type double helix at a resolution of 2.5   Å in space group P41. Here, the structure of this sequence was determined at a significantly higher resolution of 1.65   Å in space group P41212. The differences in crystal packing between the former and latter are described. The crystallographic asymmetric unit consists of one tetradecanucleotide duplex that spans more than one full turn of the A-helix. This structure allowed the unambiguous identification of solvent interactions. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - June 18, 2014 Category: Biochemistry Authors: Purushothaman, M. Varghese, A. Mandal, P.K. Gautham, N. Tags: A-DNA tetradecanucleotide right handed double helix structural communications Source Type: research

Monomer structure of a hyperthermophilic β -glucosidase mutant forming a dodecameric structure in the crystal form
One of the β -glucosidases from Pyrococcus furiosus (BGLPf) is found to be a hyperthermophilic tetrameric enzyme that can degrade cellooligosaccharides. Recently, the crystal structures of the tetrameric and dimeric forms were solved. Here, a new monomeric form of BGLPf was constructed by removing the C-terminal region of the enzyme and its crystal structure was solved at a resolution of 2.8   Å in space group P1. It was discovered that the mutant enzyme forms a unique dodecameric structure consisting of two hexameric rings in the asymmetric unit of the crystal. Under biological conditions, the mutant enzyme f...
Source: Acta Crystallographica Section F - June 18, 2014 Category: Biochemistry Authors: Nakabayashi, M. Kataoka, M. Watanabe, M. Ishikawa, K. Tags: β -glucosidases thermostable enzyme intersubunit interactions Pyrococcus furiosus structural communications Source Type: research

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of glyceraldehyde-3-phosphate dehydrogenase from Streptococcus agalactiae NEM316
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an essential enzyme involved in glycolysis. Despite lacking the secretory signal sequence, this cytosolic enzyme has been found localized at the surface of several bacteria and fungi. As a surface protein, GAPDH exhibits various adhesive functions, thereby facilitating colonization and invasion of host tissues. Streptococcus agalactiae, also known as group B streptococcus (GBS), binds onto the host using its surface adhesins and causes sepsis and pneumonia in neonates. GAPDH is one of the surface adhesins of GBS binding to human plasminogen and is a virulent factor associ...
Source: Acta Crystallographica Section F - June 18, 2014 Category: Biochemistry Authors: Nagarajan, R.Ponnuraj, K. Tags: glyceraldehyde-3-phosphate dehydrogenase moonlighting group B streptococcus surface adhesin plasminogen crystallization communications Source Type: research

Crystallization and preliminary X-ray analysis of RabX3, a tandem GTPase from Entamoeba histolytica
Ras superfamily GTPases regulate signalling pathways that control multiple biological processes by modulating the GTP/GDP cycle. Various Rab GTPases, which are the key regulators of vesicular trafficking pathways, play a vital role in the survival and virulence of the enteric parasite Entamoeba histolytica. The Rab GTPases act as binary molecular switches that utilize the conformational changes associated with the GTP/GDP cycle to elicit responses from target proteins and thereby regulate a broad spectrum of cellular processes including cell proliferation, cytoskeletal assembly, nuclear transport and intracellular membrane...
Source: Acta Crystallographica Section F - June 18, 2014 Category: Biochemistry Authors: Kumar Srivastava, V.Chandra, M.Datta, S. Tags: Rab GTPases RabX3 Entamoeba histolytica crystallization communications Source Type: research

Overexpression, purification, crystallization and structure determination of AspB, a putative aspartate aminotransferase from Mycobacterium tuberculosis
A recombinant version of a putative aspartate aminotransferase, AspB (encoded by the ORF Rv3565), from Mycobacterium tuberculosis (Mtb) was overexpressed in M. smegmatis and purified to homogeneity using liquid chromatography. Crystals of AspB were grown in a condition consisting of 0.2 M ammonium phosphate monobasic, 0.1 M calcium chloride dihydrate employing the hanging-drop vapour-diffusion method at 298 K. The crystals diffracted to a limit of 2.50 Å resolution and belonged to the orthorhombic space group P212121, with unit-cell parameters a = 93.27, b = 98.19, c = 198.70 Å. The structure of AspB ...
Source: Acta Crystallographica Section F - June 18, 2014 Category: Biochemistry Authors: Saroj, D.C.Singh, K.H.Anant, A.Biswal, B.K. Tags: Mycobacterium tuberculosis AspB crystallization communications Source Type: research

Preliminary X-ray crystallographic analysis of an engineered glutamyl-tRNA synthetase from Escherichia coli
The nature of interaction between glutamyl-tRNA synthetase (GluRS) and its tRNA substrate is unique in bacteria in that many bacterial GluRS are capable of recognizing two tRNA substrates: tRNAGlu and tRNAGln. To properly understand this distinctive GluRS–tRNA interaction it is important to pursue detailed structure–function studies; however, because of the fact that tRNA–GluRS interaction in bacteria is also associated with phylum-specific idiosyncrasies, the structure–function correlation studies must also be phylum-specific. GluRS from Thermus thermophilus and Escherichia coli, which belong to ev...
Source: Acta Crystallographica Section F - June 18, 2014 Category: Biochemistry Authors: Chongdar, N.Dasgupta, S.Datta, A.B.Basu, G. Tags: glutamyl-tRNA synthetase Escherichia coli crystallization communications Source Type: research

Purification, crystallization and preliminary X-ray diffraction analysis of Imp3 in complex with an Mpp10 peptide involved in yeast ribosome biogenesis
Eukaryotic ribosome synthesis requires a vast number of transiently associated factors. Mpp10, Imp3 and Imp4 form a protein complex in the 90S pre-ribosomal particle that conducts early processing of 18S rRNA. Here, a short fragment of Mpp10 was identified to associate with and increase the solubility of Imp3. An Imp3–Mpp10 complex was co-expressed, co-purified and co-crystallized. Preliminary X-ray diffraction analysis revealed that the crystal diffracted to 2.1 Å resolution and belonged to space group P212121, with unit-cell parameters a = 51.6, b = 86.9, c = 88.7 Å. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - June 18, 2014 Category: Biochemistry Authors: Zheng, S.Ye, K. Tags: ribosome synthesis Imp3 Mpp10 90S pre-ribosome Saccharomyces cerevisiae crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction studies of La1 from Liocheles australasiae
A novel scorpion venom peptide, La1 from Liocheles australasiae, with a molecular weight of 7.8 kDa, is presumed to possess a single von Willebrand factor type C (VWC) domain, a common protein module, based on the position of eight Cys residues in its sequence. The biological function of La1 is still unknown. Deciphering its three-dimensional structure will be helpful in understanding its biological function. La1 was crystallized by the sitting-drop vapour-diffusion method using magnesium sulfate as a precipitant. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 63.0, b = 30.2, c = 32...
Source: Acta Crystallographica Section F - June 18, 2014 Category: Biochemistry Authors: Kamachi, S.Nagao, J.Miyashita, M.Nakagawa, Y.Miyagawa, H.Tada, T. Tags: venom peptide La1 Liocheles australasiae crystallization communications Source Type: research

Crystallization and preliminary crystallographic studies of the complement 1qA globular domain from zebrafish, Dare-C1qAgD
Complement 1q (C1q) is the first component of the complement system which can initiate the classical complement pathway. In human, C1q is composed of 18 polypeptide chains: six C1qA chains, six C1qB chains and six C1qC chains. Each chain has a signal peptide and is comprised of a collagen-like region and a C-terminal C1q globular domain (C1qgD), which is organized as a heterotrimer. C1qgD can recognize antigen–antibody complexes containing IgG and IgM or can bind directly to the C-reactive protein. Although the classical complement pathway is found from fish to mammals, only the human C1qgD structure has been determi...
Source: Acta Crystallographica Section F - June 18, 2014 Category: Biochemistry Authors: Yuan, H.Chen, R.Liu, Y.Tariq, M.Sun, Y.Xia, C. Tags: complement 1q A chain C1q globular domain zebrafish Danio rerio crystallization communications Source Type: research

Expression, purification and crystallization of the phosphate-binding PstS protein from Pseudomonas aeruginosa
Pseudomonas aeruginosa (PA) infections pose a serious threat to human health. PA is a leading cause of fatal lung infections in cystic fibrosis and immune-suppressed patients, of sepsis in burn victims and of nosocomial infections. An important element in PA virulence is its ability to establish biofilms that evade suppression by the host's immune system and antibiotics. PstS, a periplasmic subunit of the Pst phosphate-transport system of PA, plays a critical role in the establishment of biofilms. In some drug-resistant PA strains, PstS is secreted in large quantities from the bacteria, where it participates in the assembl...
Source: Acta Crystallographica Section F - June 18, 2014 Category: Biochemistry Authors: Neznansky, A.Opatowsky, Y. Tags: PstS Pseudomonas aeruginosa crystallization communications Source Type: research

Cloning, purification, crystallization and preliminary X-ray studies of the putative type VI secretion immunity protein Tli5 (PA5088) from Pseudomonas aeruginosa
The putative protein PA5089 from Pseudomonas aeruginosa has recently been identified as a Tle5 phospholipase effector from a type VI secretion system (T6SS), and its toxicity can be neutralized by the cognate immunity protein Tli5 (PA5088). Here, the expression, purification, crystallization and preliminary crystallographic analysis of PA5088 are reported. X-ray diffraction data were collected from selenomethionine-derivatized PA5088 crystals to a resolution of 2.55 Å. The crystals belonged to space group P21, with unit-cell parameters a = 64.002, b = 104.744, c = 90.168 Å. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - June 18, 2014 Category: Biochemistry Authors: Chen, Z.Gao, Z.Hu, H.Xu, J.Zhang, H.Dong, Y. Tags: Pseudomonas aeruginosa PA5088 crystallization communications Source Type: research

Azide inhibition of urate oxidase
The inhibition of urate oxidase (UOX) by azide was investigated by X-ray diffraction techniques and compared with cyanide inhibition. Two well characterized sites for reagents are present in the enzyme: the dioxygen site and the substrate-binding site. To examine the selectivity of these sites towards azide inhibition, several crystallization conditions were developed. UOX was co-crystallized with azide (N3) in the presence or absence of either uric acid (UA, the natural substrate) or 8-azaxanthine (8AZA, a competitive inhibitor). In a second set of experiments, previously grown orthorhombic crystals of the UOX–UA or...
Source: Acta Crystallographica Section F - June 18, 2014 Category: Biochemistry Authors: Gabison, L.Colloc'h, N.Prangé, T. Tags: urate oxidase uricase Aspergillus flavus azide cyanide uric acid 8-azaxanthine structural communications Source Type: research

Structure of d-tagatose 3-epimerase-like protein from Methanocaldococcus jannaschii
The crystal structure of a d-tagatose 3-epimerase-like protein (MJ1311p) encoded by a hypothetical open reading frame, MJ1311, in the genome of the hyperthermophilic archaeon Methanocaldococcus jannaschii was determined at a resolution of 2.64 Å. The asymmetric unit contained two homologous subunits, and the dimer was generated by twofold symmetry. The overall fold of the subunit proved to be similar to those of the d-tagatose 3-epimerase from Pseudomonas cichorii and the d-psicose 3-epimerases from Agrobacterium tumefaciens and Clostridium cellulolyticum. However, the situation at the subunit–subunit interfa...
Source: Acta Crystallographica Section F - June 18, 2014 Category: Biochemistry Authors: Uechi, K.Takata, G.Yoneda, K.Ohshima, T.Sakuraba, H. Tags: d-tagatose 3-epimerase trinuclear metal centre TIM barrel Methanocaldococcus jannaschii structural communications Source Type: research

Crystallization of dienelactone hydrolase in two space groups: structural changes caused by crystal packing
Dienelactone hydrolase (DLH) is a monomeric protein with a simple α/β-hydrolase fold structure. It readily crystallizes in space group P212121 from either a phosphate or ammonium sulfate precipitation buffer. Here, the structure of DLH at 1.85 Å resolution crystallized in space group C2 with two molecules in the asymmetric unit is reported. When crystallized in space group P212121 DLH has either phosphates or sulfates bound to the protein in crucial locations, one of which is located in the active site, preventing substrate/inhibitor binding. Another is located on the surface of the enzyme coordinated by...
Source: Acta Crystallographica Section F - June 18, 2014 Category: Biochemistry Authors: Porter, J.L.Carr, P.D.Collyer, C.A.Ollis, D.L. Tags: dienelactone hydrolase crystal packing structural communications Source Type: research

A new crystal form of a hyperthermophilic endocellulase
This article reports the crystallization of EGPf at the more physiologically relevant pH of 5.5. Structure determination showed that this new crystal form has the symmetry of space group C2. Two molecules of the enzyme are observed in the asymmetric unit. Crystal packing is weak at pH 5.5 owing to two flexible interfaces between symmetry-related molecules. Comparison of the EGPf structures obtained at pH 9.0 and pH 5.5 reveals a significant conformational difference at the active centre and in the surface loops. The interfaces in the vicinity of the flexible surface loops impact the quality of the EGPf crystal. (Source: Ac...
Source: Acta Crystallographica Section F - June 18, 2014 Category: Biochemistry Authors: Kataoka, M.Ishikawa, K. Tags: hyperthermophile endocellulase Pyrococcus furiosus structural communications Source Type: research

Recombinant production, crystallization and X-ray crystallographic structure determination of peptidyl-tRNA hydrolase from Salmonella typhimurium
Peptidyl-tRNA hydrolase (Pth; EC 3.1.1.29) from the pathogenic bacterium Salmonella typhimurium has been cloned, expressed in Escherichia coli and crystallized for X-ray analysis. Crystals were grown using hanging-drop vapor diffusion against a reservoir solution consisting of 0.03 M citric acid, 0.05 M bis-tris propane, 1% glycerol, 3% sucrose, 25% PEG 6000 pH 7.6. Crystals were used to obtain the three-dimensional structure of the native protein at 1.6 Å resolution. The structure was determined by molecular replacement of the crystallographic data processed in space group P212121 with unit-cell parameters a =...
Source: Acta Crystallographica Section F - June 18, 2014 Category: Biochemistry Authors: Vandavasi, V.Taylor-Creel, K.McFeeters, R.L.Coates, L.McFeeters, H. Tags: peptidyl-tRNA hydrolase 1 Salmonella typhimurium structural communications Source Type: research

Structure of Rhodococcus equi virulence-associated protein B (VapB) reveals an eight-stranded antiparallel β-barrel consisting of two Greek-key motifs
Members of the virulence-associated protein (Vap) family from the pathogen Rhodococcus equi regulate virulence in an unknown manner. They do not share recognizable sequence homology with any protein of known structure. VapB and VapA are normally associated with isolates from pigs and horses, respectively. To contribute to a molecular understanding of Vap function, the crystal structure of a protease-resistant VapB fragment was determined at 1.4 Å resolution. The structure was solved by SAD phasing employing the anomalous signal of one endogenous S atom and two bound Co ions with low occupancy. VapB is an eight-stra...
Source: Acta Crystallographica Section F - June 18, 2014 Category: Biochemistry Authors: Geerds, C.Wohlmann, J.Haas, A.Niemann, H.H. Tags: antiparallel β -barrel Greek-key motif Vap protein family single-wavelength anomalous dispersion Rhodococcus equi structural communications Source Type: research

Structure of d(CCCCGGTACCGGGG)2 at 1.65 Å resolution
The crystal structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 has previously been reported as an A-type double helix at a resolution of 2.5 Å in space group P41. Here, the structure of this sequence was determined at a significantly higher resolution of 1.65 Å in space group P41212. The differences in crystal packing between the former and latter are described. The crystallographic asymmetric unit consists of one tetradecanucleotide duplex that spans more than one full turn of the A-helix. This structure allowed the unambiguous identification of solvent interactions. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - June 18, 2014 Category: Biochemistry Authors: Purushothaman, M.Varghese, A.Mandal, P.K.Gautham, N. Tags: A-DNA tetradecanucleotide right handed double helix structural communications Source Type: research

Monomer structure of a hyperthermophilic β-glucosidase mutant forming a dodecameric structure in the crystal form
One of the β-glucosidases from Pyrococcus furiosus (BGLPf) is found to be a hyperthermophilic tetrameric enzyme that can degrade cellooligosaccharides. Recently, the crystal structures of the tetrameric and dimeric forms were solved. Here, a new monomeric form of BGLPf was constructed by removing the C-terminal region of the enzyme and its crystal structure was solved at a resolution of 2.8 Å in space group P1. It was discovered that the mutant enzyme forms a unique dodecameric structure consisting of two hexameric rings in the asymmetric unit of the crystal. Under biological conditions, the mutant enzyme form...
Source: Acta Crystallographica Section F - June 18, 2014 Category: Biochemistry Authors: Nakabayashi, M.Kataoka, M.Watanabe, M.Ishikawa, K. Tags: β -glucosidases thermostable enzyme intersubunit interactions Pyrococcus furiosus structural communications Source Type: research

Crystallization and preliminary X-ray crystallographic analysis of polyphenol oxidase from Juglans regia (jrPPO1)
Tyrosinase is a type 3 copper enzyme that catalyzes the ortho-hydroxylation of monophenols to diphenols as well as their subsequent oxidation to quinones, which are precursors for the biosynthesis of melanins. The first plant tyrosinase from walnut leaves (Juglans regia) was purified to homogeneity and crystallized. During the purification, two forms of the enzyme differing only in their C-termini [jrPPO1(Asp101–Pro444) and jrPPO1(Asp101–Arg445)] were obtained. The most abundant form jrPPO1(Asp101–Arg445), as described in Zekiri et al. [Phytochemistry (2014), 101, 5–15], was crystallized, resulting ...
Source: Acta Crystallographica Section F - May 28, 2014 Category: Biochemistry Authors: Zekiri, F.Bijelic, A.Molitor, C.Rompel, A. Tags: tyrosinase type 3 copper enzyme Juglans regia polyphenol oxidase crystallization communications Source Type: research

Automation in biological crystallization
Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for t...
Source: Acta Crystallographica Section F - May 27, 2014 Category: Biochemistry Authors: Shaw Stewart, P.Mueller-Dieckmann, J. Tags: crystallization automation crystallization communications Source Type: research

Protein expression, characterization, crystallization and preliminary X-ray crystallographic analysis of a Fic protein from Clostridium difficile
Fic domains in proteins are found in abundance in nature from the simplest prokaryotes to animals. Interestingly, Fic domains found in two virulence factors of Gram-negative bacteria have recently been demonstrated to catalyse the transfer of the AMP moiety from ATP to small host GTPases. This post-translational modification has attracted considerable interest and a role for adenylylation in pathology and physiology is emerging. This work was aimed at the structural characterization of a newly identified Fic protein of the Gram-positive bacterium Clostridium difficile. A constitutively active inhibitory helix mutant of C. ...
Source: Acta Crystallographica Section F - May 25, 2014 Category: Biochemistry Authors: Welner, D.Dedic, E.van Leeuwen, H.C.Kuijper, E.Bjerrum, M.J.Østergaard, O.Jørgensen, R. Tags: Fic protein Clostridium difficile adenylylation crystallization communications Source Type: research

Crystallization and preliminary X-ray characterization of the 2,4′-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP
The enzyme 2,4′-dihydroxyacetophenone dioxygenase (or DAD) catalyses the conversion of 2,4′-dihydroxyacetophenone to 4-hydroxybenzoic acid and formic acid with the incorporation of molecular oxygen. Whilst the vast majority of dioxygenases cleave within the aromatic ring of the substrate, DAD is very unusual in that it is involved in C—C bond cleavage in a substituent of the aromatic ring. There is evidence that the enzyme is a homotetramer of 20.3 kDa subunits each containing nonhaem iron and its sequence suggests that it belongs to the cupin family of dioxygenases. By the use of limited chymotrypsinol...
Source: Acta Crystallographica Section F - May 25, 2014 Category: Biochemistry Authors: Beaven, G.Bowyer, A.Erskine, P.Wood, S.P.McCoy, A.Coates, L.Keegan, R.Lebedev, A.Hopper, D.J.Kaderbhai, M.A.Cooper, J.B. Tags: 2,4 ′ -dihydroxyacetophenone dioxygenase limited proteolysis Alcaligenes sp. 4HAP crystallization communications Source Type: research

Preliminary time-of-flight neutron diffraction studies of Escherichia coli ABC transport receptor phosphate-binding protein at the Protein Crystallography Station
Inorganic phosphate is an essential molecule for all known life. Organisms have developed many mechanisms to ensure an adequate supply, even in low-phosphate conditions. In prokaryotes phosphate transport is instigated by the phosphate-binding protein (PBP), the initial receptor for the ATP-binding cassette (ABC) phosphate transporter. In the crystal structure of the PBP–phosphate complex, the phosphate is completely desolvated and sequestered in a deep cleft and is bound by 13 hydrogen bonds: 12 to protein NH and OH donor groups and one to a carboxylate acceptor group. The carboxylate plays a key recognition role by...
Source: Acta Crystallographica Section F - May 25, 2014 Category: Biochemistry Authors: Sippel, K.H.Bacik, J.Quiocho, F.A.Fisher, S.Z. Tags: phosphate-binding protein Escherichia coli phosphate-binding protein (PBP) crystallization communications Source Type: research

Preliminary joint X-ray and neutron protein crystallographic studies of ecDHFR complexed with folate and NADP+
A crystal of Escherichia coli dihydrofolate reductase (ecDHFR) complexed with folate and NADP+ of 4 × 1.3 × 0.7 mm (3.6 mm3) in size was obtained by sequential application of microseeding and macroseeding. A neutron diffraction data set was collected to 2.0 Å resolution using the IMAGINE diffractometer at the High Flux Isotope Reactor within Oak Ridge National Laboratory. A 1.6 Å resolution X-ray data set was also collected from a smaller crystal at room temperature. The neutron and X-ray data were used together for joint refinement of the ecDHFR–folate–NADP+ ternary-complex stru...
Source: Acta Crystallographica Section F - May 25, 2014 Category: Biochemistry Authors: Wan, Q.Kovalevsky, A.Y.Wilson, M.A.Bennett, B.C.Langan, P.Dealwis, C. Tags: Escherichia coli dihydrofolate reductase protonation state crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of the peripheral light-harvesting complex LH2 from Marichromatium purpuratum
LH2 from the purple photosynthetic bacterium Marichromatium (formerly known as Chromatium) purpuratum is an integral membrane pigment–protein complex that is involved in harvesting light energy and transferring it to the LH1–RC `core' complex. The purified LH2 complex was crystallized using the sitting-drop vapour-diffusion method at 294 K. The crystals diffracted to a resolution of 6 Å using synchrotron radiation and belonged to the tetragonal space group I4, with unit-cell parameters a = b = 109.36, c = 80.45 Å. The data appeared to be twinned, producing apparent diffraction symmetry I422. T...
Source: Acta Crystallographica Section F - May 24, 2014 Category: Biochemistry Authors: Cranston, L.J.Roszak, A.W.Cogdell, R.J. Tags: Marichromatium purpuratum LH2 peripheral light-harvesting complex crystallization communications Source Type: research

Preliminary crystallographic studies of a Schistosoma mansoni antigen (Sm21.7) dynein light-chain (DLC) domain
Schistosomiasis is an inflammatory chronic disease that represents a major health problem in tropical and subtropical countries. The drug of choice for treatment, praziquantel, is effective in killing adult worms but fails to kill immature forms and prevent reinfection. One prominent antigen candidate for an anti-schistosomiasis vaccine is the protein Sm21.7 (184 amino-acid residues) from Schistosoma mansoni, a tegumental protein capable of reducing the worm burden in a murine immunization model. In the present work, the Sm21.7 gene was cloned and expressed in Escherichia coli and the full-length protein was purified to ho...
Source: Acta Crystallographica Section F - May 24, 2014 Category: Biochemistry Authors: Costa, M.A.F.Rodrigues, F.T.G.Chagas, B.C.A.Rezende, C.M.F.Goes, A.M.Nagem, R.A.P. Tags: Sm21.7 dynein light-chain domain Schistosoma mansoni crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of (R)-carbonyl reductase from Candida parapsilosis
The NADH-dependent (R)-carbonyl reductase from Candida parapsilosis (RCR) catalyzes the asymmetric reduction of 2-hydroxyacetophenone (HAP) to produce (R)-1-phenyl-1,2-ethanediol [(R)-PED], which is used as a versatile building block for the synthesis of pharmaceuticals and fine chemicals. To gain insight into the catalytic mechanism, the structures of complexes of RCR with ligands, including the coenzyme, are important. Here, the recombinant RCR protein was expressed and purified in Escherichia coli and was crystallized in the presence of NAD+. The crystals, which belonged to the orthorhombic space group P212121, with uni...
Source: Acta Crystallographica Section F - May 24, 2014 Category: Biochemistry Authors: Wang, S.Nie, Y.Yan, X.Ko, T.-P.Huang, C.-H.Chan, H.-C.Guo, R.-T.Xiao, R. Tags: (R)-carbonyl reductase Candida parapsilosis crystallization communications Source Type: research

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of Enpp6
Enpp (ectonucleotide phosphodiesterase/pyrophosphatase) 6 is a membrane-bound glycoprotein that hydrolyzes choline-containing compounds such as lysophosphatidylcholine and glycerophosphorylcholine, and presumably participates in choline metabolism. The catalytic domain of mouse Enpp6 was expressed in HEK293T cells, purified using the TARGET tag/P20.1-Sepharose system and crystallized. An X-ray diffraction data set was collected to 1.8 Å resolution. The crystal belonged to space group P1, with unit-cell parameters a = 63.7, b = 68.8, c = 69.7 Å, α = 60.6, β = 87.0, γ = 68.1°. Assuming th...
Source: Acta Crystallographica Section F - May 24, 2014 Category: Biochemistry Authors: Morita, J.Kato, K.Mihara, E.Ishitani, R.Takagi, J.Nishimasu, H.Aoki, J.Nureki, O. Tags: Enpp6 choline N-glycosylation crystallization communications Source Type: research

Crystallization and preliminary X-ray crystallographic analysis of a bacterial Asn-transamidosome
In this study, the Asn-transamidosome from Pseudomonas aeruginosa was reconstructed and crystallized by mixing purified GatCAB complex, AspRS and tRNAAsn. The crystal of the Asn-transamidosome belonged to space group P21, with unit-cell parameters a = 93.3, b = 186.0, c = 287.8 Å, β = 93.3°, and diffracted to 3.73 Å resolution. Preliminary X-ray crystallographic analysis showed that the asymmetric unit contained two Asn-transamidosomes, each composed of two GatCABs, one AspRS dimer and two tRNAAsns, indicating that the construction of the current Asn-transamidosome differs from that of Thermus ther...
Source: Acta Crystallographica Section F - May 24, 2014 Category: Biochemistry Authors: Suzuki, T.Yamashita, K.Tanaka, Y.Tanaka, I.Yao, M. Tags: transamidosome aminoacyl-tRNA AspRS GatCAB Asn-tRNAAsn Pseudomonas aeruginosa crystallization communications Source Type: research

Expression, purification, crystallization and preliminary X-ray analysis of the HER3–9E12 Fab complex
9E12 is a fully human immunoglobulin G1/κ monoclonal antibody that is specific for the epidermal growth factor receptor 3 (HER3), the overexpression of which has been detected in many tumour types and is associated with poor survival outcomes. To date, knowledge of the molecular mechanism for targeted antibodies that directly inhibit HER3 signalling is limited. Because knowledge of such therapeutic antibodies would help basic immunological therapeutics, structural insights into the HER3–9E12 Fab complex are important. Recombinant human HER3 and Fab fragments of the 9E12 antibody were cloned, expressed and cryst...
Source: Acta Crystallographica Section F - May 24, 2014 Category: Biochemistry Authors: He, K.Huang, A.Huang, Y.Takeda, H. Tags: HER3 targeted therapy crystallization communications Source Type: research

Crystallization and preliminary X-ray crystallographic studies of dehydroascorbate reductase (DHAR) from Oryza sativa L. japonica
In this study, recombinant OsDHAR protein was purified and crystallized using the sitting-drop vapour-diffusion method at pH 8.0 and 298 K. Plate-shaped crystals were obtained using 0.15 M potassium bromide, 30%(w/v) PEG MME 2000 as a precipitant, and the crystals diffracted to a resolution of 1.9 Å on beamline 5C at the Pohang Accelerator Laboratory. The X-ray diffraction data indicated that the crystal contained one OsDHAR molecule in the asymmetric unit and belonged to space group P21 with unit-cell parameters a = 47.03, b = 48.38, c = 51.83 Å, β = 107.41°. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - May 24, 2014 Category: Biochemistry Authors: Do, H.Kim, I.-S.Kim, Y.-S.Shin, S.-Y.Kim, J.-J.Mok, J.-E.Park, S.-I.Wi, A.R.Park, H.Kim, H.-W.Yoon, H.-S.Lee, J.H. Tags: ascorbate dehydroascorbate reductase Oryza sativa L. japonica crystallization communications Source Type: research