+Open data
-Basic information
Entry | Database: PDB / ID: 3pku | ||||||
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Title | Urate oxidase under 1 MPa / 10 bars pressure of nitrous oxide | ||||||
Components | Uricase | ||||||
Keywords | OXIDOREDUCTASE / T-fold / Oxidase / Peroxisome / tetramer / uric acid degradation | ||||||
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: 1.75 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 | 3pku.cif.gz | 78.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pku.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 3pku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/3pku ftp://data.pdbj.org/pub/pdb/validation_reports/pk/3pku | HTTPS FTP |
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-Related structure data
Related structure data | 3pjkC 3pk3C 3pk4C 3pk5C 3pk6C 3pk8C 3pkfC 3pkgC 3pkhC 3pkkC 3pklC 3pksC 3pktC 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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 194 molecules
#2: Chemical | ChemComp-AZA / |
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#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-N2O / |
#6: 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: 2.97 Å3/Da / Density % sol: 58.62 % |
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Crystal grow | Temperature: 298 K / Method: batch / pH: 8.5 Details: 10-15 mg/ml urate oxidase, 2mg/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: BM14 / Wavelength: 0.976 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 15, 2007 / Details: Mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. obs: 41022 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rsym value: 0.044 / Net I/σ(I): 34 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 5.5 / Num. unique all: 3756 / Rsym value: 0.2 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY Starting model: PDB entry 2IBA Resolution: 1.75→14.97 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.771 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.09 / 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: 20.808 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→14.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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