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Open data
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Basic information
Entry | Database: PDB / ID: 3bjp | ||||||
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Title | Urate oxidase cyanide uric acid ternary complex | ||||||
![]() | Uricase | ||||||
![]() | OXIDOREDUCTASE / uric acid / cyanide / inhibition / degradation mechanism / Acetylation / Peroxisome / Purine metabolism | ||||||
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. / Prange, T. / Colloc'h, N. / El Hajji, M. / Castro, B. / Chiadmi, M. | ||||||
![]() | ![]() 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 | ![]() | 79 KB | Display | ![]() |
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PDB format | ![]() | 57.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 392.4 KB | Display | ![]() |
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Full document | ![]() | 393.1 KB | Display | |
Data in XML | ![]() | 7.6 KB | Display | |
Data in CIF | ![]() | 12.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bk8C ![]() 2icqS 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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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34157.551 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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-Non-polymers , 5 types, 238 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/CYN.gif)
![](data/chem/img/ACE.gif)
![](data/chem/img/URC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CYN.gif)
![](data/chem/img/ACE.gif)
![](data/chem/img/URC.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NA / |
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#3: Chemical | ChemComp-CYN / |
#4: Chemical | ChemComp-ACE / |
#5: Chemical | ChemComp-URC / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: 8.5MG/ML URATE OXIDASE, 0.2M SODIUM CYANIDE, 50MM TRIS BUFFER, 0.5MG/ML URIC ACID, 10% PEG 8000, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 12, 2007 / Details: BENT MIRROR |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 35679 / Num. obs: 32677 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 4.1 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 4.1 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ICQ Resolution: 1.8→30 Å / Num. parameters: 10499 / Num. restraintsaints: 9869 / Isotropic thermal model: isotropic / 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: 4 / Occupancy sum hydrogen: 2312 / Occupancy sum non hydrogen: 2612 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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