+Open data
-Basic information
Entry | Database: PDB / ID: 3p9f | ||||||
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Title | Urate oxidase-azaxanthine-azide ternary complex | ||||||
Components | Uricase | ||||||
Keywords | OXYGEN BINDING / INHIBITION / DEGRADATION MECHANISM / PEROXISOME / PURINE METABOLISM / HETEROTETRAMER / OXYGEN BINDING OXIDOREDUCTASE | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Gabison, L. / Colloc'H, N. / El Hajji, M. / Castro, B. / Chiadmi, M. / Prange, T. | ||||||
Citation | Journal: To be Published Title: Azide and cyanide have different inhibition modes of urate oxidase Authors: Gabison, L. / Colloc'h, N. / El Hajji, M. / Castro, B. / Chiadmi, M. / Prange, T. #1: Journal: Bmc Struct.Biol. / Year: 2008 Title: Structural analysis of urate oxidase in complex with its natural substrate inhibited by cyanide: mechanistic implications. Authors: Gabison, L. / Prange, T. / Colloc'h, N. / El Hajji, M. / Castro, B. / Chiadmi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p9f.cif.gz | 83 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p9f.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 3p9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p9f_validation.pdf.gz | 434.9 KB | Display | wwPDB validaton report |
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Full document | 3p9f_full_validation.pdf.gz | 435.8 KB | Display | |
Data in XML | 3p9f_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 3p9f_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/3p9f ftp://data.pdbj.org/pub/pdb/validation_reports/p9/3p9f | HTTPS FTP |
-Related structure data
Related structure data | 3l8wS 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 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 | #4: Chemical | ChemComp-NA / | #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: 2.82 Å3/Da / Density % sol: 57.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 10 Details: 50 MM TRIS BUFFER, 0.3 M SODIUM AZIDE, SATURATED WITH AZAXANTHINE, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.982 / Wavelength: 0.982 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2009 / Details: BENT MIRROR |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.982 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→26.7 Å / Num. all: 43877 / Num. obs: 43286 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 4.5 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.4 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3L8W Resolution: 1.7→10 Å / Num. parameters: 10995 / Num. restraintsaints: 9911 / Cross valid method: FREE R / σ(F): 2 / σ(I): 4 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 8 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2715.6 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
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Refine LS restraints |
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