+Open data
-Basic information
Entry | Database: PDB / ID: 3pkh | ||||||
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Title | Urate oxidase under 1.5 MPa / 15 bars pressure of xenon | ||||||
Components | Uricase | ||||||
Keywords | OXIDOREDUCTASE / T-fold / Oxidase / Peroxisome / tetramer / uric acid degradation | ||||||
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: 1.71 Å | ||||||
Authors | Marassio, G. / Colloc'h, N. / Prange, T. / Abraini, J.H. | ||||||
Citation | Journal: Faseb J. / Year: 2011 Title: Pressure-response analysis of anesthetic gases xenon and nitrous oxide on urate oxidase: a crystallographic study. Authors: Marassio, G. / Prange, T. / David, H.N. / Sopkova-de Oliveira Santos, J. / Gabison, L. / Delcroix, N. / Abraini, J.H. / Colloc'h, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pkh.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pkh.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 3pkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/3pkh ftp://data.pdbj.org/pub/pdb/validation_reports/pk/3pkh | HTTPS FTP |
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-Related structure data
Related structure data | 3pjkC 3pk3C 3pk4C 3pk5C 3pk6C 3pk8C 3pkfC 3pkgC 3pkkC 3pklC 3pksC 3pktC 3pkuC 3pleC 3plgC 3plhC 3pliC 3pljC 3plmC 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-AZA / | ||
#3: Chemical | ChemComp-NA / | ||
#4: Chemical | #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: 2.99 Å3/Da / Density % sol: 58.86 % |
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Crystal grow | Temperature: 298 K / Method: batch / pH: 8.5 Details: 10-15 mg/ml Urate oxidase, 2 mg/ml 8-azaxanthine, 50 mM Tris/HCl pH 8.5, 5-8 % PEG 8000, 0-0.05 M NaCl, BATCH, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 6, 2010 / Details: MIRRORS |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 44320 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Rsym value: 0.031 / Net I/σ(I): 32.7 |
Reflection shell | Resolution: 1.71→1.8 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 10.3 / Rsym value: 0.159 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY Starting model: PDB entry 2IBA Resolution: 1.71→19.49 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.573 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.083 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.363 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→19.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.71→1.754 Å / Total num. of bins used: 20
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