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- PDB-5frc: Structure of urate oxidase prepared by the 'soak-and-freeze' meth... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5frc | ||||||
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Title | Structure of urate oxidase prepared by the 'soak-and-freeze' method under 42 bar of oxygen pressure | ||||||
![]() | URICASE | ||||||
![]() | OXIDOREDUCTASE / URATE OXIDASE / DIOXYGEN / PRESSURE / FLASH FREEZING | ||||||
Function / homology | ![]() purine nucleobase catabolic process / factor-independent urate hydroxylase / urate oxidase activity / urate catabolic process / peroxisome Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lafumat, B. / Mueller-Dieckmann, C. / Colloc'h, N. / Prange, T. / Royant, A. / van der Linden, P. / Carpentier, P. | ||||||
![]() | ![]() 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. / Colloc'h, N. / Prange, T. / Royant, A. / van der Linden, P. / Carpentier, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.5 KB | Display | ![]() |
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PDB format | ![]() | 120.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.1 KB | Display | ![]() |
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Full document | ![]() | 450.3 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 25.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fsjC ![]() 5fspC ![]() 5fssC ![]() 5fstC ![]() 4po6S S: Starting model for refinement C: citing same article ( |
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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: 34183.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: URATE OXIDASE AND 8-AZAXANTHINE FROZEN UNDER 42BAR O2 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-OXY / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.34 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→47.68 Å / Num. obs: 70982 / % possible obs: 97.5 % / Observed criterion σ(I): 1.5 / Redundancy: 4.2 % / Biso Wilson estimate: 19.97 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.44→1.53 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 1.5 / % possible all: 94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4PO6 Resolution: 1.443→47.675 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 16.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.443→47.675 Å
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Refine LS restraints |
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LS refinement shell |
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