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- PDB-8ed4: Structure of the complex between the arsenite oxidase and its nat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ed4 | ||||||
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Title | Structure of the complex between the arsenite oxidase and its native electron acceptor cytochrome c552 from Pseudorhizobium sp. str. NT-26 | ||||||
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![]() | ELECTRON TRANSPORT / Complex | ||||||
Function / homology | ![]() arsenate reductase (azurin) / oxidoreductase complex / molybdopterin cofactor binding / cellular respiration / 3 iron, 4 sulfur cluster binding / 2 iron, 2 sulfur cluster binding / periplasmic space / oxidoreductase activity / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maher, M.J. / Poddar, N. | ||||||
Funding support | 1items
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![]() | ![]() Title: The structure of the complex between the arsenite oxidase from Pseudorhizobium banfieldiae sp. strain NT-26 and its native electron acceptor cytochrome c 552. Authors: Poddar, N. / Santini, J.M. / Maher, M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 872.2 KB | Display | ![]() |
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PDB format | ![]() | 698 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4 MB | Display | ![]() |
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Full document | ![]() | 4.1 MB | Display | |
Data in XML | ![]() | 164.2 KB | Display | |
Data in CIF | ![]() | 232.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1co6S ![]() 4aayS S: Starting model for refinement |
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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
-Protein , 3 types, 12 molecules ACEGBDFHIJKL
#1: Protein | Mass: 93250.445 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 17466.205 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 12736.475 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 10 types, 1780 molecules ![](data/chem/img/MGD.gif)
![](data/chem/img/4MO.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/O.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/4MO.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/O.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MGD / #5: Chemical | ChemComp-4MO / #6: Chemical | ChemComp-F3S / #7: Chemical | ChemComp-O / #8: Chemical | ChemComp-FES / #9: Chemical | #10: Chemical | ChemComp-GOL / | #11: Chemical | #12: Chemical | ChemComp-HEC / | #13: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M sodium chloride, 0.1 M HEPES pH 7.3, 18% (w/v) PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→49.23 Å / Num. obs: 214836 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.998 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.25→2.29 Å / Num. unique obs: 10599 / CC1/2: 0.915 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4AAY,1CO6 Resolution: 2.25→49.23 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.886 / SU B: 6.761 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.397 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→49.23 Å
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