+Open data
-Basic information
Entry | Database: PDB / ID: 3l9g | ||||||
---|---|---|---|---|---|---|---|
Title | Urate oxidase complexed with uric acid and chloride | ||||||
Components | Uricase | ||||||
Keywords | OXIDOREDUCTASE / URATE OXIDASE / HIGH RESOLUTION / URIC ACID / 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: 1.75 Å | ||||||
Authors | Prange, T. / Colloc'h, N. / Gabison, L. | ||||||
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: 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. #2: 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. #3: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3l9g.cif.gz | 81.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3l9g.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 3l9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3l9g_validation.pdf.gz | 443.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3l9g_full_validation.pdf.gz | 444 KB | Display | |
Data in XML | 3l9g_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 3l9g_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/3l9g ftp://data.pdbj.org/pub/pdb/validation_reports/l9/3l9g | HTTPS FTP |
-Related structure data
Related structure data | 3l8wSC 3lbgC 3ld4C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#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 |
---|
-Non-polymers , 5 types, 252 molecules
#2: Chemical | ChemComp-URC / |
---|---|
#3: Chemical | ChemComp-MRD / ( |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-NA / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.2 % |
---|---|
Crystal grow | Temperature: 291 K / Method: batch / pH: 8 Details: 0.05M TRIS BUFFER PH 8, 8% PEG 8000, BATCH, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.948 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 14, 2008 / Details: SI(111) |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.948 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→10.2 Å / Num. all: 41223 / Num. obs: 39071 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 4.7 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.053 / Net I/σ(I): 33.1 |
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3868 / Rsym value: 0.188 / % possible all: 99 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3L8W Resolution: 1.75→10 Å / Num. parameters: 10643 / Num. restraintsaints: 9920 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 8 / Occupancy sum hydrogen: 2304.5 / Occupancy sum non hydrogen: 2627.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|