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- PDB-5nqd: Arsenite oxidase AioAB from Rhizobium sp. str. NT-26 mutant AioBF108A -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nqd | |||||||||||||||
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Title | Arsenite oxidase AioAB from Rhizobium sp. str. NT-26 mutant AioBF108A | |||||||||||||||
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![]() | OXIDOREDUCTASE / Arsenite oxidase / DMSOR family / Rieske protein | |||||||||||||||
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 | ![]() ![]() ![]() | |||||||||||||||
![]() | Santos-Silva, T. / Romao, M. / Vieira, M. / Marques, A.T. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Arsenite oxidase AioAB from Rhizobium sp. str. NT-26 mutant AioBF108A Authors: Santos-Silva, T. / Romao, M. / Vieira, M. / Marques, A.T. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 805.4 KB | Display | ![]() |
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PDB format | ![]() | 642.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.1 MB | Display | ![]() |
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Full document | ![]() | 3.2 MB | Display | |
Data in XML | ![]() | 146.7 KB | Display | |
Data in CIF | ![]() | 208.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4aayS S: Starting model for refinement |
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Similar structure data |
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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: 93179.367 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 14015.482 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 12 types, 1516 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/FES.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/P33.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/FES.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/P33.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-FES / #11: Chemical | #12: Chemical | ChemComp-PEG / | #13: Chemical | #14: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7 Details: 0.1 M Hepes sodium pH 7-8, 2 % PEG 400, 2 M ammonium sulphate. PH range: 7.0-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.55 Å / Num. obs: 247069 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 13.8 % / CC1/2: 0.988 / Rpim(I) all: 0.098 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 13 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 12160 / CC1/2: 0.59 / Rpim(I) all: 0.524 / % possible all: 100 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 4aay Resolution: 2.2→49.55 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.261 / SU ML: 0.149 / SU R Cruickshank DPI: 0.2125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.18 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.92 Å2 / Biso mean: 26.045 Å2 / Biso min: 7.25 Å2
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Refinement step | Cycle: final / Resolution: 2.2→49.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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