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Yorodumi- PDB-4wqc: Thiosulfate dehydrogenase (TsdA) from Allochromatium vinosum - K2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wqc | ||||||||||||||||||||||||
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Title | Thiosulfate dehydrogenase (TsdA) from Allochromatium vinosum - K208N mutant | ||||||||||||||||||||||||
Components | Thiosulfate dehydrogenase | ||||||||||||||||||||||||
Keywords | OXIDOREDUCTASE / tetrathionate / TsdA / c-type cytochrome | ||||||||||||||||||||||||
Function / homology | Function and homology information thiosulfate dehydrogenase / thiosulfate dehydrogenase activity / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||||||||||||||||||||
Biological species | Allochromatium vinosum (bacteria) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å | ||||||||||||||||||||||||
Authors | Brito, J.A. / Denkmann, K. / Pereira, I.A.C. / Dahl, C. / Archer, M. | ||||||||||||||||||||||||
Funding support | Portugal, Germany, 7items
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Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Thiosulfate Dehydrogenase (TsdA) from Allochromatium vinosum: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO THIOSULFATE OXIDATION. Authors: Brito, J.A. / Denkmann, K. / Pereira, I.A. / Archer, M. / Dahl, C. #1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2014 Title: Production, crystallization and preliminary crystallographic analysis of Allochromatium vinosum thiosulfate dehydrogenase TsdA, an unusual acidophilic c-type cytochrome. Authors: Brito, J.A. / Gutierres, A. / Denkmann, K. / Dahl, C. / Archer, M. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wqc.cif.gz | 114.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wqc.ent.gz | 86.4 KB | Display | PDB format |
PDBx/mmJSON format | 4wqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/4wqc ftp://data.pdbj.org/pub/pdb/validation_reports/wq/4wqc | HTTPS FTP |
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-Related structure data
Related structure data | 4wq7C 4wq8C 4wq9C 4wqaC 4wqbC 4wqdC 4wqeC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 26926.254 Da / Num. of mol.: 1 / Mutation: K208N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Allochromatium vinosum (bacteria) / Strain: ATCC 17899 / DSM 180 / NBRC 103801 / D / Gene: tsdA, Alvin_0091 / Plasmid: pPR-IBAAvtsdAs / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D3RVD4, thiosulfate dehydrogenase |
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-Non-polymers , 5 types, 253 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | #5: Chemical | ChemComp-THJ / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.28 Details: 23.5% (w/v) PEG 3350, 0.1 M Bis-tris pH 6.28, 0.2 M (NH4)2SO4, 0.1 M NaI |
-Data collection
Diffraction | Mean temperature: 100.15 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.954 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→39.44 Å / Num. obs: 33997 / % possible obs: 96 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.12 |
Reflection shell | Resolution: 1.56→1.62 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.42 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→39.44 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56→39.44 Å
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Refine LS restraints |
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LS refinement shell |
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