+Open data
-Basic information
Entry | Database: PDB / ID: 5m98 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of urate oxidase from zebrafish | ||||||
Components | Uricase | ||||||
Keywords | OXIDOREDUCTASE / uric acid / urate / purine metabolism / uricolytic activities | ||||||
Function / homology | Function and homology information purine nucleobase catabolic process / factor-independent urate hydroxylase / urate oxidase activity / urate catabolic process / peroxisome / protein homotetramerization Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Zanotti, G. / Cendron, l. / Percudani, R. / Berni, R. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Catalysis and Structure of Zebrafish Urate Oxidase Provide Insights into the Origin of Hyperuricemia in Hominoids. Authors: Marchetti, M. / Liuzzi, A. / Fermi, B. / Corsini, R. / Folli, C. / Speranzini, V. / Gandolfi, F. / Bettati, S. / Ronda, L. / Cendron, L. / Berni, R. / Zanotti, G. / Percudani, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5m98.cif.gz | 443.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5m98.ent.gz | 378.3 KB | Display | PDB format |
PDBx/mmJSON format | 5m98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m98_validation.pdf.gz | 478.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5m98_full_validation.pdf.gz | 506.4 KB | Display | |
Data in XML | 5m98_validation.xml.gz | 77.4 KB | Display | |
Data in CIF | 5m98_validation.cif.gz | 105.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/5m98 ftp://data.pdbj.org/pub/pdb/validation_reports/m9/5m98 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34239.238 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: uox / Production host: Escherichia coli (E. coli) References: UniProt: Q6DG85, factor-independent urate hydroxylase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: Tris-HCl 0.1M, pH 8.5, 8% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 21, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→83.3 Å / Num. obs: 64855 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.2 / % possible all: 89 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→83.2 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.886 / SU B: 14.587 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R Free: 0.385
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.512 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.8→83.2 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|