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Open data
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Basic information
Entry | Database: PDB / ID: 3pkk | ||||||
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Title | Urate oxidase under 0.5 MPa / 5 bars pressure of xenon | ||||||
![]() | Uricase | ||||||
![]() | OXIDOREDUCTASE / T-fold / Oxidase / Peroxisome / tetramer / uric acid degradation | ||||||
Function / homology | ![]() purine nucleobase catabolic process / factor-independent urate hydroxylase / urate oxidase activity / urate catabolic process / peroxisome Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Marassio, G. / Colloc'h, N. / Prange, T. / Abraini, J.H. | ||||||
![]() | ![]() Title: Pressure-response analysis of anesthetic gases xenon and nitrous oxide on urate oxidase: a crystallographic study. Authors: Marassio, G. / Prange, T. / David, H.N. / Sopkova-de Oliveira Santos, J. / Gabison, L. / Delcroix, N. / Abraini, J.H. / 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 KB | Display | ![]() |
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PDB format | ![]() | 57.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3pjkC ![]() 3pk3C ![]() 3pk4C ![]() 3pk5C ![]() 3pk6C ![]() 3pk8C ![]() 3pkfC ![]() 3pkgC ![]() 3pkhC ![]() 3pklC ![]() 3pksC ![]() 3pktC ![]() 3pkuC ![]() 3pleC ![]() 3plgC ![]() 3plhC ![]() 3pliC ![]() 3pljC ![]() 3plmC ![]() 2ibaS 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q00511, factor-independent urate hydroxylase |
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#2: Chemical | ChemComp-AZA / |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-XE / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.76 % |
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Crystal grow | Temperature: 298 K / Method: batch / pH: 8.5 Details: 10-15 mg/ml Urate oxidase, 2 mg/ml 8-azaxanthine, 50 mM Tris/HCl pH 8.5, 5-8 % PEG 8000, 0-0.05 M NaCl, BATCH, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 4, 2008 / Details: MIRRORS |
Radiation | Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→30 Å / Num. obs: 42090 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rsym value: 0.041 / Net I/σ(I): 29.2 |
Reflection shell | Resolution: 1.73→1.79 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.259 / % possible all: 94.2 |
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Processing
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Refinement | Method to determine structure: RIGID BODY Starting model: PDB entry 2IBA Resolution: 1.733→14.99 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.71 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 20.481 Å2
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Refinement step | Cycle: LAST / Resolution: 1.733→14.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.733→1.777 Å / Total num. of bins used: 20
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