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Yorodumi- PDB-4n9m: Joint neutron/x-ray structure of urate oxidase in complex with 8-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n9m | ||||||
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Title | Joint neutron/x-ray structure of urate oxidase in complex with 8-hydroxyxanthine | ||||||
Components | Uricase | ||||||
Keywords | OXIDOREDUCTASE / urate oxidase / uricase oxidoreductase | ||||||
Function / homology | Function and homology information purine nucleobase catabolic process / factor-independent urate hydroxylase / urate oxidase activity / urate catabolic process / peroxisome Similarity search - Function | ||||||
Biological species | Aspergillus flavus (mold) | ||||||
Method | NEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / Resolution: 2.023 Å | ||||||
Authors | Oksanen, E. / Blakeley, M.P. / Budayova-Spano, M. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: The neutron structure of urate oxidase resolves a long-standing mechanistic conundrum and reveals unexpected changes in protonation. Authors: Oksanen, E. / Blakeley, M.P. / El-Hajji, M. / Ryde, U. / Budayova-Spano, M. #1: Journal: J R Soc Interface / Year: 2009 Title: Large crystal growth by thermal control allows combined X-ray and neutron crystallographic studies to elucidate the protonation states in Aspergillus flavus urate oxidase. Authors: Oksanen, E. / Blakeley, M.P. / Bonnete, F. / Dauvergne, M.T. / Dauvergne, F. / Budayova-Spano, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n9m.cif.gz | 133 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n9m.ent.gz | 111.7 KB | Display | PDB format |
PDBx/mmJSON format | 4n9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n9m_validation.pdf.gz | 406.1 KB | Display | wwPDB validaton report |
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Full document | 4n9m_full_validation.pdf.gz | 406.1 KB | Display | |
Data in XML | 4n9m_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 4n9m_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/4n9m ftp://data.pdbj.org/pub/pdb/validation_reports/n9/4n9m | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#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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#2: Chemical | ChemComp-8HX / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-NA / |
#5: Chemical | ChemComp-DOD / |
-Experimental details
-Experiment
Experiment |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.67 % |
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Crystal grow | Temperature: 291 K / Method: temperature-controlled batch / pH: 8.5 Details: 5 % PEG 8000, 0.1 M NACL, 0.1 M TRISHCL PD 8.5, 8 MG/ML URATE OXIDASE, temperature-controlled batch, temperature 291K |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Entry-ID: 4N9M
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Reflection shell |
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-Processing
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Refinement | Baniso 12: 0 Å2 / Baniso 13: 0 Å2 / Baniso 23: -0 Å2 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL
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Refinement step | Cycle: LAST / Resolution: 2.298→40.067 Å
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Refine LS restraints |
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LS refinement shell |
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