Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystallization and preliminary X-ray analysis of the hypothetical deaminase RPB_0146 from Rhodopseudomonas palustris HaA2.

ABSTRACT: RPB_0146, a putative deaminase from Rhodopseudomonas palustris HaA2, was expressed in Escherichia coli BL21 (DE3) cells and purified using a His6 tag by Ni2+-chelating affinity chromatography for X-ray crystallographic analysis. Diffraction-quality crystals were grown by the hanging-drop vapour-diffusion method at 289?K and diffracted to a resolution of 2.44?Å using a wavelength of 1.000?Å at the Photon Factory (KEK), Japan. The crystals belonged to the orthorhombic space group P2?2?2?, with unit-cell parameters a=66.26, b=123.94, c=155.95?Å.

SUBMITTER: Zhang G

PROVIDER: S-EPMC4231866 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Crystallization and preliminary X-ray analysis of the hypothetical deaminase RPB_0146 from Rhodopseudomonas palustris HaA2.

Zhang Guofang G Yu Dan D Yang Guodong G Dong Hui H Zhang Tongcun T Liu Xiang X

Acta crystallographica. Section F, Structural biology communications 20141031 Pt 11

RPB_0146, a putative deaminase from Rhodopseudomonas palustris HaA2, was expressed in Escherichia coli BL21 (DE3) cells and purified using a His6 tag by Ni2+-chelating affinity chromatography for X-ray crystallographic analysis. Diffraction-quality crystals were grown by the hanging-drop vapour-diffusion method at 289 K and diffracted to a resolution of 2.44 Å using a wavelength of 1.000 Å at the Photon Factory (KEK), Japan. The crystals belonged to the orthorhombic space group P2₁2₁2₁, with uni ...[more]

PMID: 25372831

Similar Datasets

Crystallization and preliminary X-ray diffraction studies of a ferredoxin reductase from Rhodopseudomonas palustris CGA009.

Project description:Palustrisredoxin reductase from Rhodopseudomonas palustris CGA009, a member of the oxygenase-coupled NADH-dependent ferredoxin reductase (ONFR) family, catalyzes electron transfer from NADH to ferredoxins. It is an essential component of the cytochrome P450 systems in R. palustris CGA009, a model organism with diverse metabolic pathways. Here, the crystallization of palustrisredoxin reductase is reported. The crystals belong to the trigonal space group P3(2)21, with unit-cell parameters a = 107.5, b = 107.5, c = 69.9 A, and diffract to 2.2 A resolution on a synchrotron source.

| S-EPMC2335014 | biostudies-literature

Purification, crystallization and preliminary crystallographic analysis of cytochrome P450 203A1 from Rhodopseudomonas palustris.

Project description:Cytochrome P450 enzymes constitute a large family of haemoproteins that catalyze the monooxygenation of a great variety of endogenous and exogenous organic compounds. Cytochrome P450 203A1 (CYP203A1, RPA1009) from the metabolically versatile organism Rhodopseudomonas palustris binds a broad range of substrates, in particular substituted aromatic compounds. Crystals of CYP203A1 suitable for X-ray crystallography have been obtained and diffraction data were collected in-house to 2.0 A resolution from a single crystal. The crystals belong to space group P222, with unit-cell parameters a = 40.1, b = 95.1, c = 99.0 A, alpha = beta = gamma = 90 degrees. There is one protein molecule per asymmetric unit.

| S-EPMC2330210 | biostudies-literature

Cloning, expression, crystallization and crystallographic analysis of CouR from Rhodopseudomonas palustris.

Project description:CouR from Rhodopseudomonas palustris is a member of the MarR transcriptional regulator family. It regulates the expression of CouA and CouB, enzymes that are involved in the degradation of p-coumarate. In vivo, CouR binds to a DNA fragment containing the couAB promoter and suppresses the expression of CouA and CouB, while binding of p-coumaroyl-CoA attenuates its affinity towards DNA and activates the expression of CouA and CouB. Here, the crystallization and X-ray diffraction analyses of CouR alone and in complex with p-coumaroyl-CoA are reported. Apo and ligand-complexed CouR crystals diffracted to 2.5 and 3.3 Å resolution, respectively. The crystals of apo CouR belonged to space group P22121, with unit-cell parameters a = 62.78, b = 76.15, c = 87.38 Å, whereas the crystals of the CouR-ligand complex belonged to space group P212121, with unit-cell parameters a = 61.37, b = 69.82, c = 70.32 Å. The crystals were predicted to contain two CouR molecules or CouR-ligand complexes per asymmetric unit.

| S-EPMC4631592 | biostudies-literature

Crystallization and preliminary X-ray crystallographic analysis of biodegradative threonine deaminase (TdcB) from Salmonella typhimurium.

Project description:Biodegradative threonine deaminase (TdcB) catalyzes the deamination of L-threonine to alpha-ketobutyrate, the first reaction in the anaerobic breakdown of L-threonine to propionate. Unlike the biosynthetic threonine deaminase, TdcB is insensitive to L-isoleucine and is activated by AMP. Here, the cloning of TdcB (molecular weight 36 kDa) from Salmonella typhimurium with an N-terminal hexahistidine affinity tag and its overexpression in Escherichia coli is reported. TdcB was purified to homogeneity using Ni-NTA affinity column chromatography and crystallized using the hanging-drop vapour-diffusion technique in three different crystal forms. Crystal forms I (unit-cell parameters a = 46.32, b = 55.30, c = 67.24 A, alpha = 103.09, beta = 94.70, gamma = 112.94 degrees) and II (a = 56.68, b = 76.83, c = 78.50 A, alpha = 66.12, beta = 89.16, gamma = 77.08 degrees) belong to space group P1 and contain two and four molecules of TdcB, respectively, in the asymmetric unit. Poorly diffracting form III crystals were obtained in space group C2 and based on the unit-cell volume are most likely to contain one molecule per asymmetric unit. Two complete data sets of resolutions 2.2 A (crystal form I) and 1.7 A (crystal form II) were collected at 100 K using an in-house X-ray source.

| S-EPMC2197173 | biostudies-literature

Overexpression, crystallization and preliminary X-ray crystallographic analysis of hypothetical protein SAV0479 from Staphylococcus aureus Mu50.

Project description:SAV0479, a hypothetical protein from the Mu50 strain of methicillin- and vancomycin-resistant Staphylococcus aureus, was selected for structure and function determination as part of a structural genomics project. Here, the cloning, overexpression, purification and crystallization of SAV0479 are reported. Crystals were obtained by the hanging-drop vapour-diffusion method and diffraction data were collected to a resolution of 2.8 Å. The crystals belonged to space group P3(1)21, with unit-cell parameters a = b = 81.48, c = 82.53 Å. Three monomers of SAV0479 are present in each asymmetric unit.

| S-EPMC3614165 | biostudies-literature

Crystallization and preliminary X-ray study of the deaminase AmnE from Pseudomonas sp. AP-3.

Project description:The amnE gene from Pseudomonas sp. AP-3 has been verified as encoding a deaminase with 142 amino-acid residues. In order to change the substrate specificity via structure-based protein engineering, the amnE gene, after gene-code optimization, was chemically synthesized and cloned into the expression vector pET-28a. The protein was expressed in Escherichia coli BL21 (DE3) and purified by Ni(2+)-chelating affinity chromatography. Diffraction-quality crystals were obtained using the hanging-drop vapour-diffusion method and diffracted to a resolution of 2.09 Å. The crystals belonged to the orthorhombic space group C2221, with unit-cell parameters a = 63.23, b = 88.93, c = 137.83 Å.

| S-EPMC3702332 | biostudies-literature

Crystallization and preliminary X-ray diffraction analysis of Q4DV70 from Trypanosoma cruzi, a hypothetical protein with a putative thioredoxin domain.

Project description:Q4DV70 is annotated in the Trypanosoma cruzi CL Brener genome as a hypothetical protein with a predicted thioredoxin-like fold, although the catalytic cysteine residues that are conserved in typical oxidoreductases are replaced by serine residues. Gene-expression analysis indicates that this protein is differentially expressed during the T. cruzi life cycle, suggesting that it plays an important role during T. cruzi development. The gene coding for Q4DV70 was cloned and the protein was overexpressed in Escherichia coli with an N-terminal His tag. Purification of Q4DV70 was carried out by affinity and size-exclusion chromatography and the His tag was removed by TEV protease digestion. Crystals of Q4DV70 were grown using the sitting-drop vapour-diffusion method. A diffraction data set was collected to 1.50 A resolution from a single crystal grown in 25% PEG 1500, 200 mM sodium thiocyanate pH 6.9, 10 mM phenol and 10% ethylene glycol. The crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 35.04, b = 50.32, c = 61.18 A. The Q4DV70 structure was solved by molecular replacement using protein disulfide isomerase from yeast (PDB code 2b5e) as a search model. Initial refinement of the model indicated that the solution was correct. These data are being used for refinement of the model of Q4DV70.

| S-EPMC2688432 | biostudies-literature

Crystallization and preliminary X-ray characterization of the tetrapyrrole-biosynthetic enzyme porphobilinogen deaminase from Bacillus megaterium.

Project description:The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor which is covalently linked by a thioether bridge to an invariant cysteine residue. Expression in Escherichia coli of a His-tagged form of Bacillus megaterium PBGD permitted the crystallization and preliminary X-ray analysis of the enzyme from this species at high resolution.

| S-EPMC3729171 | biostudies-literature

Crystallization and preliminary X-ray characterization of the tetrapyrrole-biosynthetic enzyme porphobilinogen deaminase from Arabidopsis thaliana.

Project description:The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses a key early step of the haem-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor which is covalently linked by a thioether bridge to an invariant cysteine residue. Since PBGD catalyses a reaction which is common to the biosynthesis of both haem and chlorophyll, structural studies of a plant PBGD enzyme offer great potential for the discovery of novel herbicides. Until recently, structural data have only been available for the Escherichia coli and human forms of the enzyme. Expression in E. coli of a codon-optimized gene for Arabidopsis thaliana PBGD has permitted for the first time the crystallization and preliminary X-ray analysis of the enzyme from a plant species at high resolution.

| S-EPMC3509971 | biostudies-literature

Crystallization and preliminary X-ray analysis of human S100A13.

Project description:S100A13 is a member of the S100 family of EF-hand-containing calcium-binding proteins and plays an important role in the secretion of fibroblast growth factor-1 and interleukin 1alpha, two pro-angiogenic factors released by the endoplasmic reticulum/Golgi-independent non-classical secretory pathway. Human S100A13 was heterologously expressed in Escherichia coli, purified and crystallized by the hanging-drop vapour-diffusion method using PEG 3350 as the precipitant. The crystals diffracted X-rays from a synchrotron-radiation source to 1.8 A resolution and the space group was assigned as primitive orthorhombic P2(1)2(1)2(1).

| S-EPMC2225202 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data