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Yorodumi- PDB-8ch9: Crystal structure of arsenite oxidase from Alcaligenes faecalis (... -
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-Basic information
Entry | Database: PDB / ID: 8ch9 | ||||||
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Title | Crystal structure of arsenite oxidase from Alcaligenes faecalis (Af Aio) bound to arsenic oxyanion | ||||||
Components | (Arsenite oxidase subunit ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE / arsenite oxidase / molybdenum cofactor / MGD / arsenic oxyanion / antimony oxyanion | ||||||
Function / homology | Function and homology information arsenate reductase (azurin) / arsenate reductase (azurin) activity / oxidoreductase complex / cellular respiration / molybdopterin cofactor binding / 3 iron, 4 sulfur cluster binding / 2 iron, 2 sulfur cluster binding / intracellular membrane-bounded organelle / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Alcaligenes faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | ||||||
Authors | Engrola, F. / Correia, M.A.S. / Romao, M.J. / Santos-Silva, T. | ||||||
Funding support | Portugal, 1items
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Citation | Journal: To Be Published Title: Crystal structure of arsenite oxidase from Alcaligenes faecalis (Af Aio) bound to arsenic oxyanion Authors: Engrola, F. / Correia, M.A.S. / Romao, M.J. / Santos-Silva, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ch9.cif.gz | 880.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ch9.ent.gz | 697.6 KB | Display | PDB format |
PDBx/mmJSON format | 8ch9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/8ch9 ftp://data.pdbj.org/pub/pdb/validation_reports/ch/8ch9 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Arsenite oxidase subunit ... , 3 types, 8 molecules ACEBDFHG
#1: Protein | Mass: 92129.836 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: aioA, aoxB, asoA / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIF4, arsenate reductase (azurin) #2: Protein | Mass: 14303.201 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: aioB, aoxA, asoB / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIF3, arsenate reductase (azurin) #3: Protein | | Mass: 92115.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: aioA, aoxB, asoA / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIF4, arsenate reductase (azurin) |
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-Non-polymers , 10 types, 3859 molecules
#4: Chemical | ChemComp-MGD / #5: Chemical | ChemComp-F3S / #6: Chemical | ChemComp-FC6 / #7: Chemical | ChemComp-4MO / #8: Chemical | ChemComp-ART / #9: Chemical | ChemComp-GOL / #10: Chemical | ChemComp-EDO / #11: Chemical | ChemComp-FES / #12: Chemical | #13: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.35 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 10% v/v PEG 6000, 0.01 M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å |
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: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→65.474 Å / Num. obs: 594307 / % possible obs: 75 % / Redundancy: 3.5 % / CC1/2: 0.997 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.43→1.56 Å / Num. unique obs: 29716 / CC1/2: 0.589 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→65.47 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.391 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 16.157 Å2
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Refinement step | Cycle: 1 / Resolution: 1.43→65.47 Å
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