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- PDB-4wq7: Thiosulfate dehydrogenase (TsdA) from Allochromatium vinosum - "a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wq7 | ||||||||||||||||||||||||
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Title | Thiosulfate dehydrogenase (TsdA) from Allochromatium vinosum - "as isolated" form | ||||||||||||||||||||||||
![]() | Thiosulfate dehydrogenase | ||||||||||||||||||||||||
![]() | OXIDOREDUCTASE / tetrathionate / TsdA / c-type cytochrome / Allochromatium vinosum | ||||||||||||||||||||||||
Function / homology | ![]() thiosulfate dehydrogenase / thiosulfate dehydrogenase activity / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Brito, J.A. / Denkmann, K. / Pereira, I.A.C. / Dahl, C. / Archer, M. | ||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.5 KB | Display | ![]() |
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PDB format | ![]() | 49.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wq8C ![]() 4wq9C ![]() 4wqaC ![]() 4wqbC ![]() 4wqcC ![]() 4wqdC ![]() 4wqeC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 26941.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.722 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→44.81 Å / Num. obs: 29056 / % possible obs: 87 % / Redundancy: 1.8 % / Biso Wilson estimate: 16.75 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.98→2.06 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.76 / % possible all: 70 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→44.81 Å
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Refine LS restraints |
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LS refinement shell |
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