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Open data
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Basic information
Entry | Database: PDB / ID: 4pr8 | ||||||
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Title | URATE OXIDASE AZIDE URIC ACID TERNARY complex | ||||||
![]() | Uricase | ||||||
![]() | OXYGEN BINDING / INHIBITION / DEGRADATION MECHANISM / PEROXISOME / PURINE METABOLISM / HETEROTETRAMER / OXIDOREDUCTASE | ||||||
Function / homology | ![]() purine nucleobase catabolic process / factor-independent urate hydroxylase / urate oxidase activity / urate catabolic process / peroxisome Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Colloc'h, N. / Prange, T. | ||||||
![]() | ![]() Title: Azide inhibition of urate oxidase. Authors: Gabison, L. / Colloc'h, N. / 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. / Hajji, M.E. / Castro, B. / Chiadmi, M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.3 KB | Display | ![]() |
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PDB format | ![]() | 133.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.6 KB | Display | ![]() |
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Full document | ![]() | 446.3 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4oqcC ![]() 4poeC ![]() 4puvC ![]() 4fskS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34183.590 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-296 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-URC / | ||||
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.08 % |
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Crystal grow | Temperature: 291 K / Method: batch method / pH: 8.5 Details: URATE OXIDASE COMPLEXED WITH 8-NITROXANTHINE (RED CRYSTALS-3LD4) SOAKED IN URIC ACID SOLUTION. AFTER LIGAND EXCHANGE, (COLORLESS CRYSTALS) THE CRYSTALS WERE INCUBATED WITH SODIUM AZIDE 0.3M, ...Details: URATE OXIDASE COMPLEXED WITH 8-NITROXANTHINE (RED CRYSTALS-3LD4) SOAKED IN URIC ACID SOLUTION. AFTER LIGAND EXCHANGE, (COLORLESS CRYSTALS) THE CRYSTALS WERE INCUBATED WITH SODIUM AZIDE 0.3M, 18% PEG8000, TRIS BUFFER PH=8.5 FOR 1/2 H., BATCH METHOD, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2014 / Details: BENT MIRROR | |||||||||||||||||||||
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.938 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.158→47 Å / Num. all: 65154 / Num. obs: 65154 / % possible obs: 80.8 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 | |||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FSK Resolution: 1.16→11 Å / Num. parameters: 18181 / Num. restraintsaints: 21705 / σ(F): 4 StereochEM target val spec case: NONE OTHER REFINEMENT REMARKS: MAIN CHAIN ATOMS (C, N, O, CA) ANISOTROPICALLY REFINED AS WELL AS WATER MOLECULES AND SODIUM ION. HYDROGENS KEPT AT THEORETICAL PLACES Stereochemistry target values: ENGH AND HUBER Details: MAIN CHAIN ATOMS (C, N, O, CA) ANISOTROPICALLY REFINED AS WELL AS WATER MOLECULES AND SODIUM ION. HYDROGENS KEPT AT THEORETICAL PLACES
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Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 2294 / Occupancy sum non hydrogen: 2684.4 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.16→11 Å
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Refine LS restraints |
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