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Yorodumi- PDB-3cku: Urate oxidase from aspergillus flavus complexed with its inhibito... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cku | ||||||
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Title | Urate oxidase from aspergillus flavus complexed with its inhibitor 8-azaxanthin and chloride | ||||||
Components | Uricase | ||||||
Keywords | OXIDOREDUCTASE / URIC ACID DEGRADATION / 8-AZAXHANTIN | ||||||
Function / homology | Function and homology information purine nucleobase catabolic process / factor-independent urate hydroxylase / urate oxidase activity / urate catabolic process / peroxisome Similarity search - Function | ||||||
Biological species | Aspergillus flavus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Colloc'h, N. / Prange, T. | ||||||
Citation | Journal: Biophys.J. / Year: 2008 Title: Oxygen pressurized X-ray crystallography: probing the dioxygen binding site in cofactorless urate oxidase and implications for its catalytic mechanism. Authors: Colloc'h, N. / Gabison, L. / Monard, G. / Altarsha, M. / Chiadmi, M. / Marassio, G. / Sopkova-de Oliveira Santos, J. / El Hajji, M. / Castro, B. / Abraini, J.H. / 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. #2: 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. #3: Journal: Biophys.J. / Year: 2007 Title: Protein crystallography under xenon and nitrous oxide pressure: comparison with in vivo pharmacology studies and implications for the mechanism of inhaled anesthetic action. Authors: Colloc'h, N. / Sopkova-de Oliveira Santos, J. / Retailleau, P. / Vivares, D. / Bonnete, F. / Langlois d'Estainto, B. / Gallois, B. / Brisson, A. / Risso, J.J. / Lemaire, M. / Prange, T. / Abraini, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cku.cif.gz | 81.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cku.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 3cku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cku_validation.pdf.gz | 433.5 KB | Display | wwPDB validaton report |
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Full document | 3cku_full_validation.pdf.gz | 434.9 KB | Display | |
Data in XML | 3cku_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 3cku_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/3cku ftp://data.pdbj.org/pub/pdb/validation_reports/ck/3cku | HTTPS FTP |
-Related structure data
Related structure data | 2zkaC 2zkbC 3cksC 1r4sS 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: 34183.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus flavus (mold) / Genus: UAZ, UOX / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: Q00511, factor-independent urate hydroxylase |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-AZA / |
#5: 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: 2.87 Å3/Da / Density % sol: 57.08 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2MG/ML 8-AZAXANTHIN, 0.3M SODIUM CHLORIDE, 0.05M TRIS/HCL, 10-15% W/V PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.964 / Wavelength: 0.964 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2007 / Details: BENT MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.964 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→10 Å / Num. all: 43251 / Num. obs: 42048 / % possible obs: 99.63 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.5 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.0555 / Rsym value: 0.0531 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 13.7 / Num. unique all: 6302 / Rsym value: 0.084 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1R4S Resolution: 1.7→10 Å / Num. parameters: 10759 / Num. restraintsaints: 9913 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 4 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 10 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2651 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
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Refine LS restraints |
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