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- PDB-8ccq: Crystal structure of arsenite oxidase from Pseudorhizobium banfie... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ccq | |||||||||
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Title | Crystal structure of arsenite oxidase from Pseudorhizobium banfieldiae str. NT-26 (NT-26 Aio) bound to antimony trioxide | |||||||||
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![]() | OXIDOREDUCTASE / arsenite oxidase / molybdenum cofactor / MGD / arsenic oxyanion / antimony oxyanion | |||||||||
Function / homology | ![]() arsenate reductase (azurin) / oxidoreductase complex / molybdopterin cofactor binding / cellular respiration / 3 iron, 4 sulfur cluster binding / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Engrola, F. / Santos-Silva, T. / Romao, M.J. / Correia, M.A.S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Arsenite oxidase in complex with antimonite and arsenite oxyanions: Insights into the catalytic mechanism. Authors: Engrola, F. / Correia, M.A.S. / Watson, C. / Romao, C.C. / Veiros, L.F. / Romao, M.J. / Santos-Silva, T. / Santini, J.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 | ![]() | 861.1 KB | Display | ![]() |
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PDB format | ![]() | 687.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 14.2 MB | Display | ![]() |
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Full document | ![]() | 14.3 MB | Display | |
Data in XML | ![]() | 176.3 KB | Display | |
Data in CIF | ![]() | 262.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8cffC ![]() 8cgsC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 93381.633 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 18369.531 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 11 types, 3621 molecules ![](data/chem/img/MGD.gif)
![](data/chem/img/O.gif)
![](data/chem/img/4MO.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SBO.gif)
![](data/chem/img/P33.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/O.gif)
![](data/chem/img/4MO.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SBO.gif)
![](data/chem/img/P33.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MGD / #4: Chemical | ChemComp-O / #5: Chemical | ChemComp-4MO / #6: Chemical | ChemComp-F3S / #7: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-PGE / | #9: Chemical | ChemComp-GOL / #10: Chemical | ChemComp-SBO / #11: Chemical | ChemComp-P33 / #12: Chemical | ChemComp-FES / #13: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 2 M ammonium sulphate, 0.1 M HEPES sodium salt pH 7.5 and 2% v/v PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→49.3 Å / Num. obs: 354714 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.997 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.89→1.98 Å / Num. unique obs: 17429 / CC1/2: 0.511 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.108 Å2
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Refinement step | Cycle: 1 / Resolution: 1.89→141.53 Å
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