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Open data
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Basic information
Entry | Database: PDB / ID: 4oqc | ||||||
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Title | Urate OXIDASE CO-CRYSTALLIZED WITH AZIDE | ||||||
![]() | Uricase | ||||||
![]() | OXYGEN BINDING / INHIBITION / DEGRADATION MECHANISM / PEROXISOME / PURINE METABOLISM / HETEROTETRAMER / COFACTORLESS OXIDASE | ||||||
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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.8 KB | Display | ![]() |
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PDB format | ![]() | 57.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418 KB | Display | ![]() |
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Full document | ![]() | 423.7 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4poeC ![]() 4pr8C ![]() 4puvC ![]() 3l8wS C: citing same article ( 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
#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.) ![]() ![]() ![]() ![]() References: UniProt: Q00511, factor-independent urate hydroxylase | ||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.85 % |
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Crystal grow | Temperature: 291 K / pH: 8.5 Details: PROTEIN AT 20 MG/ML IN 50 MM TRIS-ACETATE BUFFER, 0.3 M SODIUM AZIDE, PH 8.5 PRECIPITATING AGENT: PEG8000 18% IN TRIS BUFFER, 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 29, 2014 / Details: BENT MIRROR |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.964 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→15 Å / Num. obs: 89456 / % possible obs: 93.3 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 3.2 / % possible all: 94.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3L8W Resolution: 1.3→10 Å / Num. parameters: 10515 / Num. restraintsaints: 9792 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 2260 / Occupancy sum non hydrogen: 2610.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→10 Å
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Refine LS restraints |
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