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Yorodumi- PDB-7a0l: Joint neutron/X-ray room temperature structure of perdeuterated A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a0l | ||||||
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Title | Joint neutron/X-ray room temperature structure of perdeuterated Aspergillus flavus urate oxidase in complex with the 8-azaxanthine inhibitor and catalytic water bound in the peroxo hole | ||||||
Components | UricaseUrate oxidase | ||||||
Keywords | OXIDOREDUCTASE / COFACTOR-FREE OXIDASE / INHIBITOR / CATALYTIC WATER / DIOXYGEN BINDING | ||||||
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 / NEUTRON DIFFRACTION / NUCLEAR REACTOR / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å | ||||||
Authors | McGregor, L. / Bui, S. / Blakeley, M.P. / Steiner, R.A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Iucrj / Year: 2021 Title: Joint neutron/X-ray crystal structure of a mechanistically relevant complex of perdeuterated urate oxidase and simulations provide insight into the hydration step of catalysis. Authors: McGregor, L. / Foldes, T. / Bui, S. / Moulin, M. / Coquelle, N. / Blakeley, M.P. / 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 | 7a0l.cif.gz | 253.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a0l.ent.gz | 191.6 KB | Display | PDB format |
PDBx/mmJSON format | 7a0l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/7a0l ftp://data.pdbj.org/pub/pdb/validation_reports/a0/7a0l | HTTPS FTP |
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-Related structure data
Related structure data | 4d12S S: Starting model for refinement |
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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: 34288.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus flavus (mold) / Gene: uaZ, uox / Production host: Escherichia coli (E. coli) References: UniProt: Q00511, factor-independent urate hydroxylase |
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#2: Chemical | ChemComp-AZA / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.7 % |
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Crystal grow | Temperature: 291 K / Method: batch mode / pH: 7.6 / Details: TRIS-Acetate, PEG 8000, 8AZA |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Biso Wilson estimate: 16.6 Å2 / Entry-ID: 7A0L
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Reflection shell |
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-Processing
Software |
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Refinement |
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Refinement step | Cycle: LAST / Resolution: 1.33→35.51 Å
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Refine LS restraints |
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LS refinement shell |
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