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Yorodumi- PDB-2iba: Urate oxidase from Aspergillus flavus complexed with its inhibito... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iba | ||||||
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Title | Urate oxidase from Aspergillus flavus complexed with its inhibitor 8-azaxanthine | ||||||
Components | Uricase | ||||||
Keywords | OXIDOREDUCTASE / uric acid degradation / T-fold domain / tetrameric enzyme | ||||||
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 / RIGID BODY / Resolution: 1.5 Å | ||||||
Authors | Colloc'h, N. / Retailleau, P. / Sopkova-de Oliveira Santos, J. / Prange, T. | ||||||
Citation | 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. / Langlois d'Estainto, B. / Gallois, B. / Brisson, A. / Risso, J.J. / Lemaire, M. / Abraini, J.H. #1: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iba.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iba.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 2iba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2iba_validation.pdf.gz | 435.2 KB | Display | wwPDB validaton report |
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Full document | 2iba_full_validation.pdf.gz | 436.5 KB | Display | |
Data in XML | 2iba_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 2iba_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/2iba ftp://data.pdbj.org/pub/pdb/validation_reports/ib/2iba | HTTPS FTP |
-Related structure data
Related structure data | 2ic0C 2icqC 2ie6C 2ie7C 1r51S 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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Details | functionnal homotetramer |
-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) / Gene: uaZ, uox / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: Q00511, factor-independent urate hydroxylase |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-AZA / |
#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: 2.98 Å3/Da / Density % sol: 58.69 % |
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Crystal grow | Temperature: 298 K / pH: 8.5 Details: 10MG/ML URATE OXIDASE, 8-AZAXANTHINE 0.2MG/ML, TRIS 20mM, PEG 8000 7%, NACL 200mM, batch, TEMPERATURE 298K, PH 8.5 |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.972 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 4, 2005 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 65481 / Num. obs: 59653 / % possible obs: 91.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Biso Wilson estimate: 18.06 Å2 / Rmerge(I) obs: 0.056 / Χ2: 0.726 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.271 / Num. unique all: 5710 / Χ2: 0.367 / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY Starting model: PDB ENTRY 1R51 Resolution: 1.5→14.87 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.147 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.872 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→14.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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