+Open data
-Basic information
Entry | Database: PDB / ID: 4op6 | ||||||
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Title | Urate OXIDASE + 8-AZAXANTHINE UNDER 40 BARS OXYGEN | ||||||
Components | Uricase | ||||||
Keywords | OXIDOREDUCTASE / HOMOTETRAMER / T-FOLD DOMAIN / PURINE METABOLISM / OXYGEN BINDING / URIC ACID / PEROXISOME | ||||||
Function / homology | Function and homology information purine nucleobase catabolic process / factor-independent urate hydroxylase / urate oxidase activity / urate catabolic process / peroxisome Similarity search - Function | ||||||
Biological species | Aspergillus flavus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY / Resolution: 1.65 Å | ||||||
Authors | Colloc'h, N. / Prange, T. | ||||||
Citation | Journal: Febs Lett. / Year: 2014 Title: Functional relevance of the internal hydrophobic cavity of urate oxidase. Authors: Colloc'h, N. / Prange, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4op6.cif.gz | 78.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4op6.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 4op6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4op6_validation.pdf.gz | 445 KB | Display | wwPDB validaton report |
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Full document | 4op6_full_validation.pdf.gz | 446 KB | Display | |
Data in XML | 4op6_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 4op6_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/4op6 ftp://data.pdbj.org/pub/pdb/validation_reports/op/4op6 | HTTPS FTP |
-Related structure data
Related structure data | 4op9C 2ibaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34183.590 Da / Num. of mol.: 1 / Fragment: UNP residues 2-302 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus flavus (mold) / Gene: uaZ, uox / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: Q00511, factor-independent urate hydroxylase |
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#2: Chemical | ChemComp-AZA / |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-OXY / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.48 % |
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Crystal grow | Temperature: 291 K / Method: batch / pH: 8.5 Details: 10-15MG/ML URATE OXIDASE, 8-AZAXANTHINE IN EXCESS, 50MM TRIS ACETATE, 5-8% PEG8000, pH 8.5, BATCH, temperature 291K |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.945 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 22, 2012 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.945 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→70 Å / Num. obs: 49104 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 33.6 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 5 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2417 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY Starting model: 2IBA Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.444 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.075 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.618 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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