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Yorodumi- PDB-7qar: Serial crystallography structure of cofactor-free urate oxidase i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qar | ||||||
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Title | Serial crystallography structure of cofactor-free urate oxidase in complex with the 5-peroxo derivative of 9-methyl uric acid at room temperature | ||||||
Components | UricaseUrate oxidase | ||||||
Keywords | OXIDOREDUCTASE / COFACTOR-FREE OXIDASE / REACTION INTERMEDIATE / SERIAL CRYSTALLOGRAPHY / DIOXYGEN | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Bui, S. / Catapano, L. / Zielinski, K. / Yefanov, O. / Murshudov, G.N. / Oberthuer, D. / Steiner, R.A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Iucrj / Year: 2022 Title: Rapid and efficient room-temperature serial synchrotron crystallography using the CFEL TapeDrive. Authors: Zielinski, K.A. / Prester, A. / Andaleeb, H. / Bui, S. / Yefanov, O. / Catapano, L. / Henkel, A. / Wiedorn, M.O. / Lorbeer, O. / Crosas, E. / Meyer, J. / Mariani, V. / Domaracky, M. / White, ...Authors: Zielinski, K.A. / Prester, A. / Andaleeb, H. / Bui, S. / Yefanov, O. / Catapano, L. / Henkel, A. / Wiedorn, M.O. / Lorbeer, O. / Crosas, E. / Meyer, J. / Mariani, V. / Domaracky, M. / White, T.A. / Fleckenstein, H. / Sarrou, I. / Werner, N. / Betzel, C. / Rohde, H. / Aepfelbacher, M. / Chapman, H.N. / Perbandt, M. / Steiner, R.A. / Oberthuer, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qar.cif.gz | 80.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qar.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7qar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/7qar ftp://data.pdbj.org/pub/pdb/validation_reports/qa/7qar | HTTPS FTP |
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-Related structure data
Related structure data | 7zpvC 7zq0C 8af4C 8af5C 8af6C 8af7C 8af8C 4cw2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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-XDS / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.11 % |
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Crystal grow | Temperature: 291 K / Method: batch mode / pH: 7.6 / Details: TRIS-ACETATE, PEG 8000, MUA, |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→17.07 Å / Num. obs: 18280 / % possible obs: 99.98 % / Redundancy: 28.2 % / CC1/2: 0.849 / CC star: 0.958 / R split: 0.3668 / Net I/σ(I): 2.44 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 20.6 % / Mean I/σ(I) obs: 0.52 / Num. unique obs: 1796 / CC1/2: 0.225 / CC star: 0.606 / R split: 1.9369 / % possible all: 100 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CW2 Resolution: 2.3→17.07 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / SU B: 14.576 / SU ML: 0.297 / Cross valid method: FREE R-VALUE / ESU R: 0.309 / ESU R Free: 0.24 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.703 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→17.07 Å
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Refine LS restraints |
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LS refinement shell |
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