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Yorodumi- PDB-2zka: Urate oxidase complexed with 8-azaxanthine under 1.0 MPa oxygen p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zka | ||||||
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Title | Urate oxidase complexed with 8-azaxanthine under 1.0 MPa oxygen pressure | ||||||
Components | Uricase | ||||||
Keywords | OXIDOREDUCTASE / URIC ACID DEGRADATION / GAZ-PROTEIN COMPLEX / T-FOLD DOMAUN / Acetylation / Peroxisome / Purine metabolism / tetramer | ||||||
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 / rigid body / Resolution: 1.61 Å | ||||||
Authors | Colloc'h, N. / Gabison, L. / Chiadmi, M. / Abraini, J.H. / 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. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zka.cif.gz | 78.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zka.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zka_validation.pdf.gz | 441.7 KB | Display | wwPDB validaton report |
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Full document | 2zka_full_validation.pdf.gz | 443.2 KB | Display | |
Data in XML | 2zka_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 2zka_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/2zka ftp://data.pdbj.org/pub/pdb/validation_reports/zk/2zka | HTTPS FTP |
-Related structure data
Related structure data | 2zkbC 3cksC 3ckuC 2ibaS C: citing same article (ref.) S: Starting model for refinement |
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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) / 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: Chemical | ChemComp-OXY / |
#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: 2.98 Å3/Da / Density % sol: 58.67 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 10mg/ml urate oxidase, 0.2mg/ml 8-azaxanthine, 50mM Tris, 20mM NaCl, PEG 8000 4-10%, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 5, 2005 / Details: mirrors |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→50 Å / Num. all: 53004 / Num. obs: 52656 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 18.39 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.61→1.67 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 3 / Num. unique all: 5211 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: rigid body Starting model: 2IBA Resolution: 1.61→14.97 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.342 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.073 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 20.42 Å2
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Refinement step | Cycle: LAST / Resolution: 1.61→14.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.608→1.65 Å / Total num. of bins used: 20
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