+Open data
-Basic information
Entry | Database: PDB / ID: 3l8w | ||||||
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Title | Urate oxidase from aspergillus flavus complexed with xanthin | ||||||
Components | Uricase | ||||||
Keywords | OXIDOREDUCTASE / URIC ACID DEGRADATION / XANTHINE / INHIBITION ASPERGILLUS FLAVUS / Peroxisome / Purine metabolism | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1 Å | ||||||
Authors | Prange, T. / Gabison, L. / Colloc'h, N. / Chiadmi, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: Near-atomic resolution structures of urate oxidase complexed with its substrate and analogues: the protonation state of the ligand. Authors: Gabison, L. / Chiadmi, M. / El Hajji, M. / Castro, B. / Colloc'h, N. / Prange, T. #1: Journal: Nat.Struct.Biol. / Year: 1997 Title: Crystal structure of the protein drug urate oxidase-inhibitor complex at 2.05 A resolution. Authors: Colloc'h, N. / El Hajji, M. / Bachet, B. / L'Hermite, G. / Schiltz, M. / Castro, B. / Mornon, J.P. #2: Journal: Febs Lett. / Year: 2006 Title: Recapture of [S]-allantoin, the product of the two-step degradation of uric acid, by urate oxidase. Authors: Gabison, L. / Chiadmi, M. / Colloc'h, N. / Castro, B. / El Hajji, M. / Prange, T. #3: Journal: Bmc Struct.Biol. / Year: 2008 Title: Structural analysis of urate oxidase in complex with its natural substrate inhibited by cyanide: mechanistic implications. Authors: Gabison, L. / Prange, T. / Colloc'h, N. / El Hajji, M. / Castro, B. / Chiadmi, M. #4: 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l8w.cif.gz | 203.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l8w.ent.gz | 165.3 KB | Display | PDB format |
PDBx/mmJSON format | 3l8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/3l8w ftp://data.pdbj.org/pub/pdb/validation_reports/l8/3l8w | HTTPS FTP |
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-Related structure data
Related structure data | 3l9gC 3lbgC 3ld4C 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33524.758 Da / Num. of mol.: 1 / Fragment: UNP residues 2-296 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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#2: Chemical | ChemComp-XAN / |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-4PO / |
#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: 2.94 Å3/Da / Density % sol: 58.14 % |
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Crystal grow | Temperature: 291 K / Method: batch / pH: 8 Details: Tris buffer 0.05M, 8% PEG 8000, pH 8.0, Batch, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.964 / Wavelength: 0.964 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2008 / Details: CURVATED MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.964 Å / Relative weight: 1 |
Reflection | Resolution: 1→29.4 Å / Num. all: 202725 / Num. obs: 153725 / % possible obs: 95.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 5.4 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.051 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1→1.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 3.7 / Num. unique all: 25556 / Rsym value: 0.199 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1R51 Resolution: 1→25 Å / Num. parameters: 25827 / Num. restraintsaints: 31137 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: CONSTRAINED ANISOTROPIC REFINEMENT
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Refine analyze | Num. disordered residues: 20 / Occupancy sum hydrogen: 2290 / Occupancy sum non hydrogen: 2841 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→25 Å
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Refine LS restraints |
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