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Yorodumi- PDB-4cw3: Crystal structure of cofactor-free urate oxidase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cw3 | ||||||
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Title | Crystal structure of cofactor-free urate oxidase in complex with the 5-peroxo derivative of 9-metyl uric acid (X-ray dose, 665 kGy) | ||||||
Components | URICASEUrate oxidase | ||||||
Keywords | OXIDOREDUCTASE / COFACTOR-FREE OXIDASE | ||||||
Function / homology | Function and homology information urate oxidase activity / factor-independent urate hydroxylase / urate catabolic process / purine nucleobase metabolic process / peroxisome Similarity search - Function | ||||||
Biological species | ASPERGILLUS FLAVUS (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.34 Å | ||||||
Authors | Bui, S. / Steiner, R.A. | ||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2014 Title: Direct evidence for a peroxide intermediate and a reactive enzyme-substrate-dioxygen configuration in a cofactor-free oxidase. Authors: Bui, S. / von Stetten, D. / Jambrina, P.G. / Prange, T. / Colloc'h, N. / de Sanctis, D. / Royant, A. / Rosta, E. / Steiner, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cw3.cif.gz | 165 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cw3.ent.gz | 139.6 KB | Display | PDB format |
PDBx/mmJSON format | 4cw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/4cw3 ftp://data.pdbj.org/pub/pdb/validation_reports/cw/4cw3 | HTTPS FTP |
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-Related structure data
Related structure data | 4cw0C 4cw2C 4cw6C 4d12C 4d13C 4d17C 4d19C 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34199.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ASPERGILLUS FLAVUS (mold) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) References: UniProt: Q00511, factor-independent urate hydroxylase |
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-Non-polymers , 5 types, 621 molecules
#2: Chemical | ChemComp-XDS / ( |
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#3: Chemical | ChemComp-MPD / ( |
#4: Chemical | ChemComp-OXY / |
#5: Chemical | ChemComp-MUA / |
#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: 2.9 Å3/Da / Density % sol: 57.4 % / Description: NONE |
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Crystal grow | pH: 8 / Details: LIKE PDB CODE 4CW2, pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2013 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→50 Å / Num. obs: 88740 / % possible obs: 100 % / Observed criterion σ(I): -1 / Redundancy: 6.5 % / Biso Wilson estimate: 7.15 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.34→1.39 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.34→70.33 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.353 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.036 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.952 Å2
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Refinement step | Cycle: LAST / Resolution: 1.34→70.33 Å
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Refine LS restraints |
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