Structure of a DsbF homologue from Corynebacterium diphtheriae
In this study, the crystal structure of a DsbE or DsbF homologue protein from Corynebacterium diphtheriae has been determined, which revealed a thioredoxin-like domain with a typical CXXC active site. Structural comparison with M. tuberculosis DsbF would help in understanding the function of the C. diphtheriae protein. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 29, 2014 Category: Biochemistry Authors: Um, S.-H.Kim, J.-S.Lee, K.Ha, N.-C. Tags: Dsb family disulfide isomerase Gram-positive bacteria structural communications Source Type: research

Structure of glutathione S-transferase 1 from the major human hookworm parasite Necator americanus (Na-GST-1) in complex with glutathione
Glutathione S-transferase 1 from Necator americanus (Na-GST-1) is a vaccine candidate for hookworm infection that has a high affinity for heme and metal porphyrins. As part of attempts to clarify the mechanism of heme detoxification by hookworm GSTs, co-crystallization and soaking studies of Na-GST-1 with the heme-like molecules protoporphyrin IX disodium salt, hematin and zinc protoporphyrin were undertaken. While these studies did not yield the structure of the complex of Na-GST-1 with any of these molecules, co-crystallization experiments resulted in the first structures of the complex of Na-GST-1 with the substrate glu...
Source: Acta Crystallographica Section F - August 29, 2014 Category: Biochemistry Authors: Asojo, O.A.Ceccarelli, C. Tags: glutathione S-transferase Necator americanus structural communications Source Type: research

High-resolution crystal structures of alternate forms of the human CD44 hyaluronan-binding domain reveal a site for protein interaction
Two new crystal structures of the extracellular hyaluronan-binding domain of human CD44 are described at high resolution. A hexagonal crystal form at 1.60 Å resolution and a monoclinic form at 1.08 Å resolution both have two molecules in the asymmetric unit arranged about a similar noncrystallographic twofold axis of symmetry. These structures are compared with those previously reported at 2.20 Å resolution to show that the fold is quite resistant to structural deformation in different crystal environments. Unexpectedly, a short peptide is found in the monoclinic crystals at a site remote from the k...
Source: Acta Crystallographica Section F - August 29, 2014 Category: Biochemistry Authors: Liu, L.-K.Finzel, B. Tags: CD44 hyaluronan-binding domain structural communications Source Type: research

Structure of nucleoside diphosphate kinase from pacific shrimp (Litopenaeus vannamei) in binary complexes with purine and pyrimidine nucleoside diphosphates
Nucleoside diphosphate kinase (NDK; EC 2.7.4.6) is an enzyme that catalyzes the third phosphorylation of nucleoside diphosphates, leading to nucleoside triphosphates for DNA replication. Expression of the NDK from Litopenaeus vannamei (LvNDK) is known to be regulated under viral infection. Also, as determined by isothermal titration calorimetry, LvNDK binds both purine and pyrimidine deoxynucleoside diphosphates with high binding affinity for dGDP and dADP and with no heat of binding interaction for dCDP [Quintero-Reyes et al. (2012), J. Bioenerg. Biomembr. 44, 325–331]. In order to investigate the differences in sel...
Source: Acta Crystallographica Section F - August 29, 2014 Category: Biochemistry Authors: López-Zavala, A.A.Quintero-Reyes, I.E.Carrasco-Miranda, J.S.Stojanoff, V.Weichsel, A.Rudiño-Piñera, E.Sotelo-Mundo, R.R. Tags: nucleoside diphosphate kinase deoxyadenine binary complex shrimp Litopenaeus vannamei structural communications Source Type: research

Structural basis for the inhibition of poly(ADP-ribose) polymerases 1 and 2 by BMN 673, a potent inhibitor derived from dihydropyridophthalazinone
Poly(ADP-ribose) polymerases 1 and 2 (PARP1 and PARP2), which are involved in DNA damage response, are targets of anticancer therapeutics. BMN 673 is a novel PARP1/2 inhibitor with substantially increased PARP-mediated tumor cytotoxicity and is now in later-stage clinical development for BRCA-deficient breast cancers. In co-crystal structures, BMN 673 is anchored to the nicotinamide-binding pocket via an extensive network of hydrogen-bonding and π-stacking interactions, including those mediated by active-site water molecules. The novel di-branched scaffold of BMN 673 extends the binding interactions towards the outer ed...
Source: Acta Crystallographica Section F - August 29, 2014 Category: Biochemistry Authors: Aoyagi-Scharber, M.Gardberg, A.S.Yip, B.K.Wang, B.Shen, Y.Fitzpatrick, P.A. Tags: poly(ADP-ribose) polymerase PARP inhibitor BMN 673 inhibitor design structural communications Source Type: research

Carboplatin binding to histidine
Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the bromine form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl c...
Source: Acta Crystallographica Section F - August 29, 2014 Category: Biochemistry Authors: Tanley, S.W.M.Diederichs, K.Kroon-Batenburg, L.M.J.Levy, C.Schreurs, A.M.M.Helliwell, J.R. Tags: carboplatin histidine avoid partial conversion to cisplatin NaBr crystallization conditions non-NaCl crystallization conditions model protein (hen egg-white lysozyme) structural communications Source Type: research

The binding of platinum hexahalides (Cl, Br and I) to hen egg-white lysozyme and the chemical transformation of the PtI6 octahedral complex to a PtI3 moiety bound to His15
This study examines the binding and chemical stability of the platinum hexahalides K2PtCl6, K2PtBr6 and K2PtI6 when soaked into pre-grown hen egg-white lysozyme (HEWL) crystals as the protein host. Direct comparison of the iodo complex with the chloro and bromo complexes shows that the iodo complex is partly chemically transformed to a square-planar PtI3 complex bound to the Nδ atom of His15, a chemical behaviour that is not exhibited by the chloro or bromo complexes. Each complex does, however, bind to HEWL in its octahedral form either at one site (PtI6) or at two sites (PtBr6 and PtCl6). As heavy-atom derivatives ...
Source: Acta Crystallographica Section F - August 29, 2014 Category: Biochemistry Authors: Tanley, S.W.M.Starkey, L.-V.Lamplough, L.Kaenket, S.Helliwell, J.R. Tags: platinum hexahalides hen egg-white lysozyme PtI3 ligand bound to histidine X-ray lasers structural communications Source Type: research

Chemical conversion of cisplatin and carboplatin with histidine in a model protein crystallized under sodium iodide conditions
Cisplatin and carboplatin are platinum anticancer agents that are used to treat a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine in hen egg-white lysozyme (HEWL) showed a partial chemical conversion of carboplatin to cisplatin owing to the high sodium chloride concentration used in the crystallization conditions. Also, the co-crystallization of HEWL with carboplatin in sodium bromide conditions resulted in the partial conversion of carboplatin to the transbromoplatin form, with a portion of the cyclobutanedicarboxylate (CBDC) moiety still present. The results of the co-cryst...
Source: Acta Crystallographica Section F - August 29, 2014 Category: Biochemistry Authors: Tanley, S.W.M.Helliwell, J.R. Tags: cisplatin carboplatin sodium iodide crystallization histidine transiodoplatin (PtI2X2) PtI3X species structural communications Source Type: research

Microseed matrix screening for optimization in protein crystallization: what have we learned?
In conclusion, MMS is a simple, time- and cost-efficient optimization method that is applicable to many recalcitrant crystallization problems. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 29, 2014 Category: Biochemistry Authors: D'Arcy, A.Bergfors, T.Cowan-Jacob, S.W.Marsh, M. Tags: microseed matrix screening optimization crystallization crystallization communications Source Type: research

Crystallization, preliminary X-ray crystallographic and cryo-electron microscopy analysis of a bifunctional enzyme fucokinase/l-fucose-1-P-guanylyltransferase from Bacteroides fragilis
In this study, both recombinant F-FKP and C-FKP were expressed and purified. Size-exclusion chromatography experiments and analytical ultracentrifugation results showed that both F-FKP and C-FKP are trimers. Native F-FKP protein was crystallized by the vapour-diffusion method and the crystals belonged to space group P212121 and diffracted synchrotron X-rays to 3.7 Å resolution. The crystal unit-cell parameters are a = 91.36, b = 172.03, c = 358.86 Å, α = β = γ = 90.00°. The three-dimensional features of the F-FKP molecule were observed by cryo-EM (cryo-electron microscopy). The prelimin...
Source: Acta Crystallographica Section F - August 28, 2014 Category: Biochemistry Authors: Cheng, C.Gu, J.Su, J.Ding, W.Yin, J.Liang, W.Yu, X.Ma, J.Wang, P.G.Xiao, Z.Liu, Z.-J. Tags: FKP Bacteroides fragilis cryo-EM crystallization communications Source Type: research

Molecular replacement with a large number of molecules in the asymmetric unit
The exponential increase in protein structures deposited in the Protein Data Bank (PDB) has resulted in the elucidation of most, if not all, protein folds, thus making molecular replacement (MR) the most frequently used method for structure determination. A survey of the PDB shows that most of the structures determined by molecular replacement contain less than ten molecules in the asymmetric unit and that it is predominantly virus and ribosome structures that contain more than 20 molecules in the asymmetric unit. While the success of the MR method depends on several factors, such as the homology and the size of an input m...
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Jobichen, C.Swaminathan, K. Tags: large number of molecules in the asymmetric unit molecular replacement strategies for structure determination laboratory communications Source Type: research

Expression, purification, crystallization and preliminary X-ray diffraction analysis of acylpeptide hydrolase from Deinococcus radiodurans
Acylpeptide hydrolase (APH; EC 3.4.19.1), which belongs to the S9 family of serine peptidases (MEROPS), catalyzes the removal of an N-acylated amino acid from a blocked peptide. The role of this enzyme in mammalian cells has been suggested to be in the clearance of oxidatively damaged proteins as well as in the degradation of the β-amyloid peptides implicated in Alzheimer's disease. Detailed structural information for the enzyme has been reported from two thermophilic archaea; both of the archaeal APHs share a similar monomeric structure. However, the mechanisms of substrate selectivity and active-site accessibility a...
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Are, V.N.Ghosh, B.Kumar, A.Yadav, P.Bhatnagar, D.Jamdar, S.N.Makde, R.D. Tags: acylpeptide hydrolase Deinococcus radiodurans S9 serine peptidase crystallization communications Source Type: research

Crystallization and preliminary X-ray analysis of two variants of the Escherichia coli O157 ParE2–PaaA2 toxin–antitoxin complex
The paaR2–paaA2–parE2 operon is a three-component toxin–antitoxin module encoded in the genome of the human pathogen Escherichia coli O157. The toxin (ParE2) and antitoxin (PaaA2) interact to form a nontoxic toxin–antitoxin complex. In this paper, the crystallization and preliminary characterization of two variants of the ParE2–PaaA2 toxin–antitoxin complex are described. Selenomethionine-derivative crystals of the full-length ParE2–PaaA2 toxin–antitoxin complex diffracted to 2.8 Å resolution and belonged to space group P41212 (or P43212), with unit-cell parameters a ...
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Sterckx, Y.G.J.Haesaerts, S.Van Melderen, L.Loris, R. Tags: ParE2 – PaaA2 toxin antitoxin Escherichia coli O157 crystallization communications Source Type: research

Crystallization and preliminary X-ray crystallographic analysis of the PH-GRAM domain of human MTMR4
In this study, the PH-GRAM domain of human MTMR4 was cloned, overexpressed in Escherichia coli, purified and crystallized by the vapour-diffusion method. The crystals diffracted to 3.20 Å resolution at a synchrotron beamline and belonged to either space group P61 or P65, with unit-cell parameters a = b = 109.10, c = 238.97 Å. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Lee, J.U.Son, J.Y.Yoo, K.-Y.Shin, W.Im, D.-W.Kim, S.J.Ryu, S.E.Heo, Y.-S. Tags: myotubularin-related proteins MTMR4 phosphoinositide phosphatase PH-GRAM domain crystallization communications Source Type: research

Cloning, purification and preliminary crystallographic analysis of the Helicobacter pylori pseudaminic acid biosynthesis N-acetyltransferase PseH
Helicobacter pylori infection is the common cause of gastritis and duodenal and stomach ulcers, which have been linked to a higher risk of the development of gastric cancer. The motility that facilitates persistent infection requires functional flagella that are heavily glycosylated with 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno-nonulosonic acid (pseudaminic acid). Pseudaminic acid biosynthesis protein H (PseH) catalyzes the third step in its biosynthetic pathway, producing UDP-2,4-diacetamido-2,4,6-trideoxy-β-l-altropyranose. Crystals of H. pylori PseH have been grown by the hanging-drop vapour-diffusion m...
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Liu, Y.C.Ud-Din, A.I.Roujeinikova, A. Tags: Helicobacter pylori N-acetyltransferase acetyl-CoA pseudaminic acid biosynthesis crystallization communications Source Type: research

Recombinant expression, purification, crystallization and preliminary X-ray diffraction analysis of the C-terminal DUF490963–1138 domain of TamB from Escherichia coli
In this study, the C-terminal DUF490963–1138 domain of TamB was overexpressed in Escherichia coli K-12, purified and crystallized using the sitting-drop vapour-diffusion method. The crystals belonged to the primitive trigonal space group P3121, with unit-cell parameters a = b = 57.34, c = 220.74 Å, and diffracted to 2.1 Å resolution. Preliminary secondary-structure and X-ray diffraction analyses are reported. Two molecules are predicted to be present in the asymmetric unit. Experimental phasing using selenomethionine-labelled protein will be undertaken in the future. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Josts, I.Grinter, R.Kelly, S.M.Mosbahi, K.Roszak, A.Cogdell, R.Smith, B.O.Byron, O.Walker, D. Tags: DUF490 TamB autotransporter Escherichia coli crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of Xaa-Pro dipeptidase from Xanthomonas campestris
Xaa-Pro dipeptidase (XPD; prolidase; EC 3.4.13.9) specifically hydrolyzes dipeptides with a prolyl residue at the carboxy-terminus. Xanthomonas spp. possess two different isoforms of XPD (48 and 43 kDa) which share ∼24% sequence identity. The XPD of 43 kDa in size (XPD43) from Xanthomonas spp. is unusual as it lacks the strictly conserved tyrosine residue (equivalent to Tyr387 in Escherichia coli aminopeptidase P) that is suggested to be important in the proton-shuttle transfer required for catalysis in the M24B (MEROPS) family. Here, the crystallization and preliminary X-ray analysis of XPD43 from X. campestris (G...
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Kumar, A.Are, V.N.Ghosh, B.Agrawal, U.Jamdar, S.N.Makde, R.D.Sharma, S.M. Tags: Xaa-Pro dipeptidase prolidase Xanthomonas campestris crystallization communications Source Type: research

Complex assembly, crystallization and preliminary X-ray crystallographic analysis of the chicken CD8αα–BF2*0401 complex
In the process of antigen presentation, the MHCI–CD8 complex is important for immune signal transduction by the activation of cytotoxic T cells. Here, the expression, purification, crystallization and X-ray analysis of the complex of the chicken MHC class I molecule BF2*0401 and CD8αα (CD8αα–BF2*0401) are reported. This complex was verified by SDS–PAGE analysis of a CD8αα–BF2*0401 crystal, which showed three bands corresponding to the molecular weights of BF2*0401, β2-microglobulin and CD8α, respectively. The crystal of CD8αα–BF2*0401 ...
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Liu, Y.Chen, R.Tariq, M.Xia, C. Tags: chicken CD8 α BF2*0401 crystallization communications Source Type: research

Purification, crystallization and preliminary X-ray crystallographic analysis of TssL from Vibrio cholerae
The type VI secretion system (T6SS) is a macromolecular complex that is conserved in Gram-negative bacteria. The T6SS secretes effector proteins into recipient cells in a contact-dependent manner in order to accomplish cooperative and competitive interactions with the cells. Although the composition and mechanism of the T6SS have been intensively investigated across many Gram-negative bacteria, to date structural information on T6SS components from the important pathogen Vibrio cholerae has been rare. Here, the cloning, purification, crystallization and preliminary X-ray crystallographic analysis of the cytoplasmic domain ...
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Jeong, J.-H.Chang, J.H.Kim, Y.G. Tags: T6SS Vibrio cholerae TssL crystallization communications Source Type: research

Purification, crystallization and preliminary crystallographic analysis of the 16S rRNA methyltransferase RsmI from Escherichia coli
RsmI and RsmH are AdoMet-dependent methyltransferases that are responsible for the 2′-O-methylation and N4-methylation of C1402 of Escherichia coli 16S rRNA, respectively. Modification of this site has been found to play a role in fine-tuning the shape and function of the P-site to increase the decoding fidelity. It is interesting to study the mechanism by which C1402 can be methylated by both RsmI and RsmH. The crystal structure of RsmH in complex with AdoMet and cytidine has recently been determined and provided some implications for N4-methylation of this site. Here, the purification and crystallization of RsmI as...
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Zhao, M.Wang, L.Zhang, H.Dong, Y.Gong, Y.Zhang, L.Wang, J. Tags: RNA modification methyltransferase RsmI AdoMet crystallization communications Source Type: research

Crystallization and preliminary X-ray analysis of the C-terminal fragment of Ski7 from Saccharomyces cerevisiae
Ski7 (superkiller protein 7) plays a critical role in the mRNA surveillance pathway. The C-terminal fragment of Ski7 (residues 520–747) from Saccharomyces cerevisiae was heterologously expressed in Escherichia coli and purified to homogeneity. It was successfully crystallized and preliminary X-ray data were collected to 2.0 Å resolution using synchrotron radiation. The crystal belonged to a trigonal space group, either P3121 or P3221, with unit-cell parameters a = b = 73.5, c = 83.6 Å. The asymmetric unit contains one molecule of the C-terminal fragment of Ski7 with a corresponding crystal volume per ...
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Lee, J.-Y.Park, S.H.Jeong, B.-C.Song, H.K. Tags: mRNA surveillance nonstop decay RNA degradation Saccharomyces cerevisiae Ski7 crystallization communications Source Type: research

Expression, purification, crystallization and preliminary X-ray analysis of glucose-1-phosphate uridylyltransferase (GalU) from Erwinia amylovora
Glucose-1-phosphate uridylyltransferase from Erwinia amylovora CFPB1430 was expressed as a His-tag fusion protein in Escherichia coli. After tag removal, the purified protein was crystallized from 100 mM Tris pH 8.5, 2 M ammonium sulfate, 5% ethylene glycol. Diffraction data sets were collected to a maximum resolution of 2.46 Å using synchrotron radiation. The crystals belonged to the hexagonal space group P62, with unit-cell parameters a = 80.67, b = 80.67, c = 169.18. The structure was solved by molecular replacement using the structure of the E. coli enzyme as a search model. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Toccafondi, M.Cianci, M.Benini, S. Tags: Erwinia GalU amylovoran uridylyltransferase UDP-glucose sugar metabolism crystallization communications Source Type: research

Purification, characterization and preliminary X-ray crystallographic studies of monodehydroascorbate reductase from Oryza sativa L. japonica
Monodehydroascorbate reductase (MDHAR; EC 1.6.5.4) is a key enzyme in the reactive oxygen species (ROS) detoxification system of plants. The participation of MDHAR in ascorbate (AsA) recycling in the ascorbate–glutathione cycle is important in the acquired tolerance of crop plants to abiotic environmental stresses. Thus, MDHAR represents a strategic target protein for the improvement of crop yields. Although physiological studies have intensively characterized MDHAR, a structure-based functional analysis is not available. Here, a cytosolic MDHAR (OsMDHAR) derived from Oryza sativa L. japonica was expressed using Esch...
Source: Acta Crystallographica Section F - August 27, 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.Lee, J.H.Yoon, H.-S.Kim, H.-W. Tags: monodehydroascorbate reductase Oryza sativa L. japonica abiotic stress ascorbate regeneration crystallization communications Source Type: research

Expression, purification, crystallization and preliminary crystallographic analysis of human myotubularin-related protein 3
Myotubularin-related proteins are a large family of phosphatases that have the catalytic activity of dephosphorylating the phospholipid molecules phosphatidylinositol 3-phosphate and phosphatidylinositol 3,5-bisphosphate. Each of the 14 family members contains a phosphatase catalytic domain, which is inactive in six family members owing to amino-acid changes in a key motif for the activity. All of the members also bear PH-GRAM domains, which have low homologies between them and have roles that are not yet clear. Here, the cloning, expression, purification and crystallization of human myotubularin-related protein 3 encompas...
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Son, J.Y.Lee, J.U.Yoo, K.-Y.Shin, W.Im, D.-W.Kim, S.J.Ryu, S.E.Heo, Y.-S. Tags: myotubularin-related proteins MTMR3 phosphoinositide phosphatase PH-GRAM domain crystallization communications Source Type: research

Crystallization and preliminary X-ray crystallographic analysis of YfcM: an important factor for EF-P hydroxylation
Elongation factor P (EF-P) plays an essential role in the translation of polyproline-containing proteins in bacteria. It becomes functional by the post-translational modification of its highly conserved lysine residue. It is first β-lysylated by PoxA and then hydroxylated by YfcM. In this work, the YfcM protein from Escherichia coli was overexpressed, purified and crystallized. The crystal of YfcM was obtained by the in situ proteolysis crystallization method and diffracted X-rays to 1.45 Å resolution. It belonged to space group C2, with unit-cell parameters a = 124.4, b = 37.0, c = 37.6 Å, β = 10...
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Kobayashi, K.Suzuki, T.Dohmae, N.Ishitani, R.Nureki, O. Tags: elongation factor P in situ proteolysis crystallization crystallization communications Source Type: research

Cloning, purification, crystallization and preliminary X-ray studies of a carbohydrate-binding module (CBM_E1) derived from sugarcane soil metagenome
In this study, CBM_E1 was expressed, purified and crystallized. X-ray diffraction data were collected to 1.95 Å resolution. The crystals, which were obtained by the sitting-drop vapour-diffusion method, belonged to space group I23, with unit-cell parameters a = b = c = 88.07 Å. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Campos, B.M.Alvarez, T.M.Liberato, M.V.Polikarpov, I.Gilbert, H.J.Zeri, A.C.M.Squina, F.M. Tags: accessory domain GH5 carbohydrate-binding module glycoside hydrolases biofuels renewable energy crystallization communications Source Type: research

Purification, crystallization and preliminary X-ray crystallographic analysis of glycosyltransferase-1 from Bacillus cereus
Glycosyltransferases (GTs), which are distributed widely in various organisms, including bacteria, fungi, plants and animals, play a role in synthesizing biological compounds. Glycosyltransferase-1 from Bacillus cereus (BcGT-1), which is capable of transferring glucose to small molecules such as kaempferol and quercetin, has been identified as a member of the family 1 glycosyltransferases which utilize uridine diphosphate glucose (UDP-glucose) as the sugar donor. BcGT-1 (molecular mass 45.5 kDa) has been overexpressed, purified and crystallized using the hanging-drop vapour-diffusion method. According to X-ray diffractio...
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Hsieh, Y.-C.Chiu, H.-H.Huang, Y.-C.Fun, H.-K.Lu, C.-Y.Li, Y.-K.Chen, C.-J. Tags: glycosyltransferase Bacillus cereus crystallization communications Source Type: research

Cloning, expression, purification, crystallization and preliminary crystallographic analysis of the C-terminal domain of Par-4 (PAWR)
Prostate apoptosis response-4 protein is an intrinsically disordered pro-apoptotic protein with tumour suppressor function. Par-4 is known for its selective induction of apoptosis in cancer cells only and its ability to interact with various apoptotic proteins via its C-terminus. Par-4, with its unique function and various interacting partners, has gained importance as a potential target for cancer therapy. The C-terminus of the rat homologue of Par-4 was crystallized and a 3.7 Å resolution X-ray diffraction data set was collected. Preliminary data analysis shows the space group to be P41212. The unit-cell paramete...
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Tiruttani Subhramanyam, U.K.Kubicek, J.Eidhoff, U.B.Labahn, J. Tags: Par-4 coiled coil leucine zipper crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of the periplasmic domain of the Escherichia coli aspartate receptor Tar and its complex with aspartate
The cell-surface receptor Tar mediates bacterial chemotaxis toward an attractant, aspartate (Asp), and away from a repellent, Ni2+. To understand the molecular mechanisms underlying the induction of Tar activity by its ligands, the Escherichia coli Tar periplasmic domain with and without bound aspartate (Asp-Tar and apo-Tar, respectively) were each crystallized in two different forms. Using ammonium sulfate as a precipitant, crystals of apo-Tar1 and Asp-Tar1 were grown and diffracted to resolutions of 2.10 and 2.40 Å, respectively. Alternatively, using sodium chloride as a precipitant, crystals of apo-Tar2 and Asp-...
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Mise, T.Matsunami, H.Samatey, F.A.Maruyama, I.N. Tags: attractant bacterial chemotaxis cell-surface receptor Escherichia coli transmembrane signalling crystallization communications Source Type: research

Crystallization and preliminary X-ray analysis of the periplasmic domain of FliP, an integral membrane component of the bacterial flagellar type III protein-export apparatus
In this study, FliPP from Thermotoga maritima (TmFliPP) and its selenomethionine derivative (SeMet-TmFliPP) were purified and crystallized. TmFliPP formed a homotetramer in solution. Crystals of TmFliPP and SeMet-TmFliPP were obtained by the hanging-drop vapour-diffusion technique with 2-methyl-2,4-pentanediol as a precipitant. These two crystals grew in the hexagonal space group P6222 or P6422, with unit-cell parameters a = b = 114.9, c = 193.8 Å. X-ray diffraction data were collected from crystals of TmFliPP and SeMet-TmFliPP to 2.4 and 2.8 Å resolution, respectively. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Fukumura, T.Furukawa, Y.Kawaguchi, T.Saijo-Hamano, Y.Namba, K.Imada, K.Minamino, T. Tags: FliP type III export apparatus bacterial flagellum Thermotoga maritima crystallization communications Source Type: research

Crystallization of the C-terminal redox domain of the sulfur-assimilatory enzyme APR1 from Arabidopsis thaliana
Plant-type APS reductase (APR), which catalyzes the reduction of activated sulfate to sulfite in plants, consists of a reductase domain and a C-terminal redox domain showing sequence homology to thioredoxin but possessing the activity of glutaredoxin. In order to understand the structural and biochemical properties of the redox domain of plant-type APS reductase, the C-terminal domain of APR1 (APR1C) from Arabidopsis thaliana was crystallized using the sitting-drop vapour-diffusion method. X-ray diffraction data were collected to a resolution of 2.70 Å on the SPXF beamline BL13B1 at the NSRRC, Taiwan. The crystals ...
Source: Acta Crystallographica Section F - August 27, 2014 Category: Biochemistry Authors: Chen, F.-F.Chang, Y.-Y.Cho, C.-C.Hsu, C.-H. Tags: glutaredoxin sulfonucleotide reductase sulfur assimilation Arabidopsis thaliana APR1 crystallization communications Source Type: research

Identifying, studying and making good use of macromolecular crystals
Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100 000 protein structures, with the majority stemming from X-ray crystallography. As the name might suggest, crystallography requires crystals. As detectors become more sensitive and X-ray sources more intense, the notion of a crystal is gradually changing from one large enough to embellish expensive jewellery to objects that have external dimensions of the order of the wavelength of visible light. Identifying these crystals...
Source: Acta Crystallographica Section F - July 25, 2014 Category: Biochemistry Authors: Calero, G.Cohen, A.E.Luft, J.R.Newman, J.Snell, E.H. Tags: crystal detection crystal growth crystal positioning crystallization communications Source Type: research

Protein crystallization with microseed matrix screening: application to human germline antibody Fabs
The crystallization of 16 human antibody Fab fragments constructed from all pairs of four different heavy chains and four different light chains was enabled by employing microseed matrix screening (MMS). In initial screening, diffraction-quality crystals were obtained for only three Fabs, while many Fabs produced hits that required optimization. Application of MMS, using the initial screens and/or refinement screens, resulted in diffraction-quality crystals of these Fabs. Five Fabs that failed to give hits in the initial screen were crystallized by cross-seeding MMS followed by MMS optimization. The crystallization protoco...
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Obmolova, G.Malia, T.J.Teplyakov, A.Sweet, R.W.Gilliland, G.L. Tags: Fabs crystallization microseed matrix screening seeding optimization automation laboratory communications Source Type: research

Crystallographic characterization of the C-terminal coiled-coil region of mouse Bicaudal-D1 (BICD1)
This report describes the crystallization and X-ray data collection of the BICD1 CC3 region, as well as the preparation of the complex of BICD1 CC3 with a constitutively active mutant of Rab6. The crystals of the BICD1 CC3 region belonged to space group C2, with unit-cell parameters a = 59.0, b = 36.8, c = 104.3 Å, α = γ = 90, β = 99.8°. The X-ray diffraction data set was collected to 1.50 Å resolution. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Terawaki, S.Ootsuka, H.Higuchi, Y.Wakamatsu, K. Tags: retrograde transport BICD1 Rab6 crystallization communications Source Type: research

Crystallization and preliminary X-ray analysis of a ribokinase from Vibrio cholerae O395
Ribokinase (RK) is one of the principal enzymes in carbohydrate metabolism, catalyzing the reaction of d-ribose and adenosine triphosphate to produce ribose-5-phosphate and adenosine diphosphate (ADP). To provide further insight into the catalytic mechanism, the rbsK gene from Vibrio cholerae O395 encoding ribokinase was cloned and the protein was overexpressed in Escherichia coli BL21 (DE3) and purified using Ni2+–NTA affinity chromatography. Crystals of V. cholerae RK (Vc-RK) and of its complex with ribose and ADP were grown in the presence of polyethylene glycol 6000 and diffracted to 3.4 and 1.75 Å resolu...
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Paul, R.Dandopath Patra, M.Banerjee, R.Sen, U. Tags: Vibrio cholerae ribokinase ribose ATP crystallization communications Source Type: research

Characterization, crystallization and preliminary X-ray crystallographic analysis of the human Uba5 C-terminus–Ufc1 complex
In this study, Uba5 residues 364–404 were demonstrated to be necessary for the transthiolation of Ufm1 to Ufc1, and Uba5 381–404 was identified to be the minimal region for Ufc1 recognition. The fusion protein between Uba5 381–404 and Ufc1 was cloned, expressed and purified, and exists as a homodimer in solution. Crystallization was performed at 293 K using PEG 4000 as precipitant; the optimized crystals diffracted to 3.0 Å resolution and had unit-cell parameters a = b = 82.49, c = 62.47 Å, α = β = 90, γ = 120°. With one fusion-protein molecule in the asymmetric unit...
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Xie, S. Tags: Uba5 Ufc1 crystallization communications Source Type: research

Purification, crystallization and preliminary X-ray crystallographic studies of Rv3705c from Mycobacterium tuberculosis
The conserved protein Rv3705c from Mycobacterium tuberculosis has been cloned, expressed, purified and crystallized by the sitting-drop vapour-diffusion method using PEG 3350 as a precipitant. The Rv3705c crystals exhibited space group P6122 or P6522, with unit-cell parameters a = b = 198.0, c = 364.1 Å, α = β = 90, γ = 120°, and diffracted to a resolution of 3.3 Å. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Lu, F.Gao, F.Li, H.Gong, W.Zhou, L.Bi, L. Tags: Mycobacterium tuberculosis Rv3705c crystallization communications Source Type: research

Crystallization and preliminary X-ray crystallographic analysis of the complex between the N-D1 domain of VCP from Homo sapiens and the N domain of OTU1 from Saccharomyces cerevisiae
VCP (valosin-containing protein; also known as p97) plays important roles in many biological processes including the ERAD (endoplasmic reticulum-associated degradation) pathway and its function is governed by binding partners. OTU1 (ovarian tumour domain-containing protein 1) is a recently discovered deubiquitinating enzyme that interacts directly with VCP in the ERAD pathway. In order to understand the interactions between the two proteins, the N-D1 domain of VCP and the UBXL domain of OTU1 were cloned, overexpressed, purified and crystallized. The crystals of the complex diffracted to 3.25 Å resolution and belong...
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Kim, S.J.Kim, E.E. Tags: VCP ATPase OTU1 UBXL domain crystallization communications Source Type: research

Crystallization and X-ray diffraction of virus-like particles from a piscine betanodavirus
In this report, crystals of DGNNV VLPs were grown to a size of 0.27 mm within two weeks by the hanging-drop vapour-diffusion method at 283 K and diffracted X-rays to ∼7.5 Å resolution. In-house X-ray diffraction data of the DGNNV VLP crystals showed that the crystals belonged to space group R32, with unit-cell parameters a = b = 353.00, c = 800.40 Å, α = β = 90, γ = 120°. 23 268 unique reflections were acquired with an overall Rmerge of 18.2% and a completeness of 93.2%. Self-rotation function maps confirmed the fivefold, threefold and twofold symmetries of the icosahedron of ...
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Luo, Y.-C.Wang, C.-H.Wu, Y.-M.Liu, W.Lu, M.-W.Lin, C.-S. Tags: Dragon grouper nervous necrosis virus (DGNNV) Betanodavirus Epinephelus lanceolatus crystallization communications Source Type: research

Expression, high-pressure refolding, purification, crystallization and preliminary X-ray analysis of a novel single-strand-specific 3′–5′ exonuclease PhoExo I from Pyrococcus horikoshii OT3
PhoExo I is a single-strand-specific 3′–5′ exonuclease from Pyrococcus horikoshii OT3 and is thought to be involved in a Thermococcales-specific DNA-repair pathway. The recombinant PhoExo I protein was produced as inclusion bodies in Escherichia coli cells. Solubilization of the inclusion bodies was performed by the high-pressure refolding method and highly purified protein was subjected to crystallization by the sitting-drop vapour-diffusion method at 20°C. A crystal of PhoExo I was obtained in a reservoir solution consisting of 0.1 M Tris–HCl pH 8.9, 27% PEG 6000 and diffracted X-rays to 1.5...
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Miyazono, K.Tsutsumi, K.Ishino, Y.Tanokura, M. Tags: nuclease PhoExo I Pyrococcus horikoshii DNA repair high-pressure refolding crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of a single variable domain of the immunoglobulin superfamily in amphioxus, Amphi-IgSF-V
Amphioxus is regarded as an essential animal model for the study of immune evolution. Discovery of new molecules with the immunoglobulin superfamily (IgSF) variable (V) domain in amphioxus would help in studying the evolution of IgSF V molecules in the immune system. A protein was found which just contains only one IgSF V domain in amphioxus, termed Amphi-IgSF-V; it has over 30% sequence identity to the V domains of human immunoglobulins and mammalian T-cell receptors. In order to clarify the three-dimensional structure of this new molecule in amphioxus, Amphi-IgSF-V was expressed, purified and crystallized, and diffractio...
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Jiang, B.Liu, Y.Chen, R.Wang, Z.Tariq, M.Xia, C. Tags: amphioxus immunoglobulin superfamily variable domain crystallization communications Source Type: research

Crystallization and preliminary crystallographic study of human coronavirus NL63 main protease in complex with an inhibitor
In this study, the main protease of human coronavirus NL63 was crystallized in complex with a Michael acceptor. The complex crystals diffracted to 2.85 Å resolution and belonged to space group P41212, with unit-cell parameters a = b = 87.2, c = 212.1 Å. Two molecules were identified per asymmetric unit. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Wang, F.Tan, Y.Li, H.Chen, X.Wang, J.Li, S.Fu, S.Zhao, Q.Chen, C.Su, D.Yang, H. Tags: human coronavirus NL63 main protease N3 inhibitor crystallization communications Source Type: research

Overexpression, purification, crystallization and preliminary X-ray characterization of the fourth scaffoldin A cohesin from Acetivibrio cellulolyticus in complex with a dockerin from a family 5 glycoside hydrolase
Cellulosomes are cell-bound multienzyme complexes secreted by anaerobic bacteria that play a crucial role in carbon turnover by degrading plant cell walls to simple sugars. Integration of cellulosomal components occurs via highly ordered protein–protein interactions between cohesin modules located in a molecular scaffold and dockerin modules found in cellulosomal enzymes. Acetivibrio cellulolyticus possesses a complex cellulosome arrangement which is organized by a primary enzyme-binding scaffoldin (ScaA), two anchoring scaffoldins (ScaC and ScaD) and an unusual adaptor scaffoldin (ScaB). A dockerin from a family 5 g...
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Bule, P.Correia, A.Cameron, K.Alves, V.D.Cardoso, V.Fontes, C.M.G.A.Najmudin, S. Tags: cellulosome cohesin dockerin Acetivibrio cellulolyticus crystallization communications Source Type: research

Overexpression, crystallization and preliminary X-ray characterization of Ruminococcus flavefaciens scaffoldin C cohesin in complex with a dockerin from an uncharacterized CBM-containing protein
Cellulosomes are massive cell-bound multienzyme complexes tethered by macromolecular scaffolds that coordinate the efforts of many anaerobic bacteria to hydrolyze plant cell-wall polysaccharides, which are a major untapped source of carbon and energy. Integration of cellulosomal components occurs via highly ordered protein–protein interactions between cohesin modules, located in the scaffold, and dockerin modules, found in the enzymes and other cellulosomal proteins. The proposed cellulosomal architecture for Ruminococcus flavefaciens strain FD-1 consists of a major scaffoldin (ScaB) that acts as the backbone to whic...
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Bule, P.Ruimy-Israeli, V.Cardoso, V.Bayer, E.A.Fontes, C.M.G.A.Najmudin, S. Tags: cellulosome cohesin dockerin Ruminococcus flavefaciens scaffoldin C crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of YidC, a membrane-protein chaperone and insertase from Bacillus halodurans
YidC, a member of the YidC/Oxa1/Alb3 family, inserts proteins into the membrane and facilitates membrane-protein folding in bacteria. YidC plays key roles in both Sec-mediated integration and Sec-independent insertion of membrane proteins. Here, Bacillus halodurans YidC2, which has five transmembrane helices conserved among the other family members, was identified as a target protein for structure determination by a fluorescent size-exclusion chromatography analysis. The protein was overexpressed, purified and crystallized in the lipidic cubic phase. The crystals diffracted X-rays to 2.4 Å resolution and belonged t...
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Kumazaki, K.Tsukazaki, T.Nishizawa, T.Tanaka, Y.Kato, H.E.Nakada-Nakura, Y.Hirata, K.Mori, Y.Suga, H.Dohmae, N.Ishitani, R.Nureki, O. Tags: YidC membrane-protein insertase lipidic cubic phase Bacillus halodurans crystallization communications Source Type: research

Preliminary X-ray crystallographic studies of the TIR domain of human Toll-like receptor 6
In this study, the human TLR6 TIR domain corresponding to amino acids 640–796 was overexpressed in Escherichia coli using engineered C-terminal His tags. The TLR6 TIR domain was then purified to homogeneity and crystallized at 20°C. Finally, X-ray diffraction data were collected to a resolution of 2.2 Å from a crystal belonging to space group C2, with unit-cell parameters a = 127.60, b = 44.20, c = 75.72 Å, β = 118.89° (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Jang, T.Park, H.H. Tags: TIR domain Toll-like receptor 6 crystallization communications Source Type: research

Expression, purification and crystallization of pecan (Carya illinoinensis) vicilin
In this study, vicilin from pecan (Carya illinoinensis) was isolated and was expressed in bacteria for the first time. The cupin structural core of the protein, residues 369–792, was purified by metal-affinity and gel-filtration chromatography to high purity. Vicilin crystals were obtained and the best crystal diffracted to 2.65 Å resolution in space group P212121. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Lee, B.Zhang, R.Du, W.-X.Grauke, L.J.McHugh, T.H.Zhang, Y.-Z. Tags: convicilin food allergen storage protein Carya illinoinensis crystallization communications Source Type: research

Cloning, expression, purification, crystallization and X-ray crystallographic analysis of d-lactate dehydrogenase from Lactobacillus jensenii
The thermostable d-lactate dehydrogenase from Lactobacillus jensenii (Ljd-LDH) is a key enzyme for the production of the d-form of lactic acid from pyruvate concomitant with the oxidation of NADH to NAD+. The polymers of lactic acid are used as biodegradable bioplastics. The Ljd-LDH protein was crystallized using the hanging-drop vapour-diffusion method in the presence of 28%(w/v) polyethylene glycol 400, 100 mM Tris–HCl pH 9, 200 mM magnesium sulfate at 295 K. X-ray diffraction data were collected to a maximum resolution of 2.1 Å. The crystal belonged to space group P3121, with unit-cell parameters a =...
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Kim, S.Kim, Y.H.Kim, K.-J. Tags: d-lactate dehydrogenase Lactobacillus jensenii polylactic acid bioplastics crystallization communications Source Type: research

Cloning, purification and preliminary crystallographic analysis of Ara127N, a GH127 β-l-arabinofuranosidase from Geobacillus stearothermophilus T6
The l-arabinan utilization system of Geobacillus stearothermophilus T6 is composed of five transcriptional units that are clustered within a 38 kb DNA segment. One of the transcriptional units contains 11 genes, the last gene of which (araN) encodes a protein, Ara127N, that belongs to the newly established GH127 family. Ara127N shares 44% sequence identity with the recently characterized HypBA1 protein from Bifidobacterium longum and thus is likely to function similarly as a β-l-arabinofuranosidase. β-l-Arabinofuranosidases are enzymes that hydrolyze β-l-arabinofuranoside linkages, the less common form of ...
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Lansky, S.Salama, R.Dann, R.Shner, I.Manjasetty, B.A.Belrhali, H.Shoham, Y.Shoham, G. Tags: Geobacillus stearothermophilus glycoside hydrolase β -arabinofuranosidase, GH127 arabinose arabinofuranoside arabinan utilization selenomethionine MAD SAD crystallization communications Source Type: research

The structure of α-haemoglobin in complex with a haemoglobin-binding domain from Staphylococcus aureus reveals the elusive α-haemoglobin dimerization interface
Adult haemoglobin (Hb) is made up of two α and two β subunits. Mutations that reduce expression of the α- or β-globin genes lead to the conditions α- or β-thalassaemia, respectively. Whilst both conditions are characterized by anaemia of variable severity, other details of their pathophysiology are different, in part owing to the greater stability of the β chains that is conferred through β self-association. In contrast, α subunits interact weakly, and in the absence of stabilizing quaternary interactions the α chain (α) is prone to haem loss and denaturation. Th...
Source: Acta Crystallographica Section F - July 23, 2014 Category: Biochemistry Authors: Krishna Kumar, K.Jacques, D.A.Guss, J.M.Gell, D.A. Tags: α -haemoglobin homodimer HbH Hb Bart's IsdHN1 Staphylococcus aureus structural communications Source Type: research