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Open data
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Basic information
Entry | Database: PDB / ID: 3p9o | ||||||
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Title | Aerobic ternary complex of urate oxidase with azide and chloride | ||||||
![]() | Uricase | ||||||
![]() | OXYGEN BINDING / URIC ACID / INHIBITION / DEGRADATION MECHANISM / PEROXISOME / PURINE METABOLISM / AZIDE / OXYGEN BINDING OXIDOREDUCTASE | ||||||
Function / homology | ![]() purine nucleobase catabolic process / factor-independent urate hydroxylase / urate oxidase activity / urate catabolic process / peroxisome Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gabison, L. / Colloc'H, N. / El Hajji, M. / Castro, B. / Chiadmi, M. / Prange, T. | ||||||
![]() | ![]() Title: Azide and Cyanide Show Different Inhibition Modes to Urate Oxidase Authors: Gabison, L. / Colloc'h, N. / El Hajji, M. / Castro, B. / Chiadmi, M. / Prange, T. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.9 KB | Display | ![]() |
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PDB format | ![]() | 61.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.9 KB | Display | ![]() |
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Full document | ![]() | 458 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 26.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3l8wS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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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.) ![]() ![]() ![]() ![]() References: UniProt: Q00511, factor-independent urate hydroxylase | ||||||
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#2: Chemical | ChemComp-AZI / #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 57.26 % |
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Crystal grow | Temperature: 291 K / pH: 10 Details: SOLUTION A (0.1 ML): 50MM TRIS BUFFER, 0.3 M SODIUM AZIDE, SATURATED WITH URIC ACID BUFFER, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 10.0 |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.45→39.7 Å / Num. obs: 69903 / % possible obs: 99.4 % / Observed criterion σ(I): 4 / Redundancy: 5.5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 3.8 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3L8W Resolution: 1.45→39.7 Å / Num. parameters: 11299 / Num. restraintsaints: 10091 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 18 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2754.95 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→39.7 Å
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Refine LS restraints |
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