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Yorodumi- PDB-7puf: urate oxidase azaxanthine complex under 600 bar (60 MPa) of argon -
+Open data
-Basic information
Entry | Database: PDB / ID: 7puf | ||||||
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Title | urate oxidase azaxanthine complex under 600 bar (60 MPa) of argon | ||||||
Components | UricaseUrate oxidase | ||||||
Keywords | OXIDOREDUCTASE / aspergillus flavus / homotetramer / argon / high pressure | ||||||
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: 1.86 Å | ||||||
Authors | Prange, T. / Colloc'h, N. / Carpentier, P. | ||||||
Funding support | 1items
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Citation | Journal: Acta Cryst. D / Year: 2022 Title: Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization Authors: Prange, T. / Carpentier, P. / Dhaussy, A.C. / Girard, E. / Colloc'h, N. #1: Journal: Current trends in X-ray crystallography / Year: 2011 Title: Current trends in X-ray Crystallography. Intech Open books Authors: Colloc'h, N. / Marassio, G. / Prange, T. #2: Journal: Journal of Applied Crystallography / Year: 2016 Title: Gas-sensitive biological crystals processed in pressurized oxygen and krypton atmospheres: deciphering gas channels in proteins using a novel soak-and-freeze methodology Authors: Lafumat, B. / Mueller-Dieckmann, C. / Leonard, G. / Colloc'h, N. / Prange, T. / Giraud, T. / Dobias, F. / Royant, A. / van der Linden, P. / Carpentier, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7puf.cif.gz | 145.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7puf.ent.gz | 112.5 KB | Display | PDB format |
PDBx/mmJSON format | 7puf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/7puf ftp://data.pdbj.org/pub/pdb/validation_reports/pu/7puf | HTTPS FTP |
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-Related structure data
Related structure data | 6i9xC 6i9zC 6ia1C 6ia3C 6ia9C 6ic1C 6rgmC 7p0cC 7p0dC 7p0gC 7pwnC 7q09C 1r51S C: citing same article (ref.) 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
#1: Protein | Mass: 33524.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus flavus (mold) / Gene: uaZ, uox / Production host: Komagataella pastoris (fungus) References: UniProt: Q00511, factor-independent urate hydroxylase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-AR / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.67 % |
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Crystal grow | Temperature: 298 K / Method: batch mode / pH: 8 Details: 20 microLiter (17 mg/mL protein, BUFFER Tris/Acetate pH 8) mixed with 20 microLiter PEG 4000 8% (same pH) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.7712 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2018 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7712 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→47.7 Å / Num. obs: 53842 / % possible obs: 81.5 % / Redundancy: 11.3 % / Biso Wilson estimate: 12.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.86→1.9 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 699 / CC1/2: 0.95 / Rpim(I) all: 0.151 / Rrim(I) all: 0.222 / % possible all: 20.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: dimer reconstructed from pdbid 1R51 Resolution: 1.86→47.68 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.558 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES :
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90 Å2 / Biso mean: 17.38 Å2 / Biso min: 5.25 Å2
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Refinement step | Cycle: final / Resolution: 1.86→47.68 Å
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Refine LS restraints |
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