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- PDB-3gko: Crystal structure of urate oxydase using surfactant Poloxamer 188... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gko | ||||||
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Title | Crystal structure of urate oxydase using surfactant Poloxamer 188 as a New Crystallizing Agent | ||||||
![]() | Uricase | ||||||
![]() | OXIDOREDUCTASE / urate oxydase / surfactant / poloxamer P188 / Acetylation / Peroxisome / Purine metabolism | ||||||
Function / homology | ![]() purine nucleobase catabolic process / factor-independent urate hydroxylase / urate oxidase activity / urate catabolic process / peroxisome Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Delfosse, V. / Giffard, M. / Sciara, G. / Bonnete, F. / Mayer, C. | ||||||
![]() | ![]() Title: Surfactant Poloxamer 188 as a New Crystallizing Agent for Urate Oxidase Authors: Giffard, M. / Delfosse, V. / Sciara, G. / Mayer, C. / Cambillau, C. / El Hajji, M. / Castro, B. / Bonnete, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.2 KB | Display | ![]() |
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PDB format | ![]() | 62 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.3 KB | Display | ![]() |
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Full document | ![]() | 449.2 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1r51S 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 on special symmetry positions |
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Components
#1: Protein | Mass: 34199.586 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 | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50mM Tris, 30mM KCl, 6% Poloxamer P188, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2007 / Details: two SESO Cnie Mirrors |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. all: 52978 / Num. obs: 52744 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 4.1 / Num. unique all: 8725 / Rsym value: 0.366 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1R51 Resolution: 1.6→29.52 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3569301 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.8415 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→29.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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