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Yorodumi- PDB-1r51: URATE OXIDASE FROM ASPERGILLUS FLAVUS COMPLEXED WITH ITS INHIBITO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r51 | |||||||||
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Title | URATE OXIDASE FROM ASPERGILLUS FLAVUS COMPLEXED WITH ITS INHIBITOR 8-AZAXANTHIN | |||||||||
Components | UricaseUrate oxidase | |||||||||
Keywords | OXIDOREDUCTASE / URIC ACID DEGRADATION / DIMERIC BARREL / TUNNEL-SHAPED PROTEIN | |||||||||
Function / homology | Function and homology information purine nucleobase catabolic process / urate oxidase activity / factor-independent urate hydroxylase / urate catabolic process / peroxisome Similarity search - Function | |||||||||
Biological species | Aspergillus flavus (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Prange, T. / Retailleau, P. / Colloc'h, N. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Complexed and ligand-free high-resolution structures of urate oxidase (Uox) from Aspergillus flavus: a reassignment of the active-site binding mode. Authors: Retailleau, P. / Colloc'h, N. / Vivares, D. / Bonnete, F. / Castro, B. / El-Hajji, M. / Mornon, J.P. / Monard, G. / Prange, T. #1: Journal: Nat.Struct.Biol. / Year: 1997 Title: Crystal Structure of the Protein Drug Urate Oxidase-Inhibitor Complex at 2.05 A Resolution Authors: Colloc'h, N. / El Hajji, M. / Bachet, B. / L'Hermite, G. / Schiltz, M. / Prange, T. / Castro, B. / Mornon, J.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r51.cif.gz | 78.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r51.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 1r51.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/1r51 ftp://data.pdbj.org/pub/pdb/validation_reports/r5/1r51 | HTTPS FTP |
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-Related structure data
Related structure data | 1r4sC 1r4uC 1r56C 1uox S: Starting model for refinement C: citing same article (ref.) |
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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: 34199.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus flavus (mold) References: UniProt: Q00511, factor-independent urate hydroxylase |
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#2: Chemical | ChemComp-AZA / |
#3: Chemical | ChemComp-CYS / |
#4: 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: 2.85 Å3/Da / Density % sol: 56.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 8.5MG/ML PROTEIN, 0.2MG/ML 8-AZAXANTHIN 5-7% W/V PEG8000, 100MM TRIS/HCL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 278 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97 / Wavelength: 0.972 Å | |||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→18 Å / Num. obs: 38367 / % possible obs: 92.1 % / Redundancy: 11.2 % / Rsym value: 0.065 / Net I/σ(I): 19.8 | |||||||||
Reflection shell | Resolution: 1.75→1.8 Å / Mean I/σ(I) obs: 4.8 / Rsym value: 0.222 / % possible all: 79.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UOX 1uox Resolution: 1.75→10 Å / Num. parameters: 10359 / Num. restraintsaints: 9753 / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2577 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→10 Å
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Refine LS restraints |
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