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Open data
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Basic information
Entry | Database: PDB / ID: 7p0d | ||||||
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Title | URATE OXIDASE WITH 8-AZAXANTHINE UNDER 310 MPA PRESSURE | ||||||
![]() | Uricase | ||||||
![]() | OXIDOREDUCTASE / HPMX / purine metabolism / tetramer / T-fold domain / peroxisome | ||||||
Function / homology | ![]() purine nucleobase catabolic process / factor-independent urate hydroxylase / urate oxidase activity / urate catabolic process / peroxisome Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Colloc'h, N. / Prange, T. / Girard, E. | ||||||
![]() | ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.3 KB | Display | ![]() |
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PDB format | ![]() | 57 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 966.8 KB | Display | ![]() |
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Full document | ![]() | 970.3 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6i9xC ![]() 6i9zC ![]() 6ia1C ![]() 6ia3C ![]() 6ia9C ![]() 6ic1C ![]() 6rgmC ![]() 7p0cC ![]() 7p0gC ![]() 7pufC ![]() 7pwnC ![]() 7q09C ![]() 4op9S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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 / Fragment: URICASE Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q00511, factor-independent urate hydroxylase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.43 % |
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Crystal grow | Temperature: 298 K / Method: batch mode / pH: 7.5 Details: 20 MG/ML URATE OXIDASE, 8-AZAXANTHINE CONCENTRATION IN EXCESS, 50 MM TRIS/ACETATE, 8% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX SX-165mm / Detector: CCD / Date: Jul 28, 2019 / Details: mirrors |
Radiation | Monochromator: SI 111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.58183 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→29.506 Å / Num. obs: 15109 / % possible obs: 96 % / Redundancy: 3.4 % / Rsym value: 0.139 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2216 / Rsym value: 0.635 / % possible all: 97.2 |
-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR | R rigid body: 0.365
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB 4OP9 Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.872 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.426 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.89 Å2 / Biso mean: 49.02 Å2 / Biso min: 25.8 Å2
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Refinement step | Cycle: final / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.46 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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