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Yorodumi- PDB-8cgs: Crystal structure of arsenite oxidase from Alcaligenes faecalis (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cgs | ||||||
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Title | Crystal structure of arsenite oxidase from Alcaligenes faecalis (Af Aio) bound to antimony oxyanion | ||||||
Components |
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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 / metal ion binding Similarity search - Function | ||||||
Biological species | Alcaligenes faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Engrola, F. / Correia, M.A.S. / Romao, M.J. / Santos-Silva, T. | ||||||
Funding support | Portugal, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cgs.cif.gz | 842.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cgs.ent.gz | 672.5 KB | Display | PDB format |
PDBx/mmJSON format | 8cgs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/8cgs ftp://data.pdbj.org/pub/pdb/validation_reports/cg/8cgs | HTTPS FTP |
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-Related structure data
Related structure data | 8ccqC 8cffC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
-Protein , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 92032.719 Da / Num. of mol.: 4 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: 14190.044 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Production host: Escherichia coli (E. coli) |
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-Non-polymers , 16 types, 3382 molecules
#3: Chemical | ChemComp-MGD / #4: Chemical | ChemComp-O / #5: Chemical | ChemComp-4MO / #6: Chemical | ChemComp-F3S / #7: Chemical | ChemComp-PEG / #8: Chemical | ChemComp-ACT / #9: Chemical | ChemComp-PO4 / #10: Chemical | ChemComp-UJI / #11: Chemical | ChemComp-CL / #12: Chemical | ChemComp-GOL / #13: Chemical | #14: Chemical | ChemComp-FES / #15: Chemical | #16: Chemical | ChemComp-SO4 / | #17: Chemical | ChemComp-NA / | #18: 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: 2.68 Å3/Da / Density % sol: 54.18 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 15% v/v PEG 4000, 0.1 M sodium citrate pH 5.5 and 0.2 M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→48.47 Å / Num. obs: 365490 / % possible obs: 95.3 % / Redundancy: 2 % / CC1/2: 0.993 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 1.84→1.87 Å / Num. unique obs: 17998 / CC1/2: 0.848 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→116.27 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.471 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.112 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.392 Å2
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Refinement step | Cycle: 1 / Resolution: 1.84→116.27 Å
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