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- PDB-4wq9: Thiosulfate dehydrogenase (TsdA) from Allochromatium vinosum - di... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wq9 | ||||||||||||||||||||||||
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Title | Thiosulfate dehydrogenase (TsdA) from Allochromatium vinosum - dithionite soak | ||||||||||||||||||||||||
![]() | Thiosulfate dehydrogenase | ||||||||||||||||||||||||
![]() | OXIDOREDUCTASE / tetrathionate / TsdA / c-type cytochrome | ||||||||||||||||||||||||
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 | ![]() | 109.7 KB | Display | ![]() |
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PDB format | ![]() | 87.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 490.4 KB | Display | ![]() |
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Full document | ![]() | 492 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wq7C ![]() 4wq8C ![]() 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 26973.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 242 molecules ![](data/chem/img/HEC.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/THJ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/THJ.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-EDO / | #6: Chemical | ChemComp-H2S / | #7: Chemical | ChemComp-THJ / | #8: Water | ChemComp-HOH / | |
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-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: Apr 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2395 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→34.96 Å / Num. obs: 66925 / % possible obs: 93 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.01 |
Reflection shell | Resolution: 1.47→1.52 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.93 / Num. unique all: 5738 / % possible all: 86 |
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.47→34.96 Å
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Refine LS restraints |
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LS refinement shell |
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