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Yorodumi- PDB-1vay: Crystal Structure of Uricase from Arthrobacter globiformis with i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vay | ||||||
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Title | Crystal Structure of Uricase from Arthrobacter globiformis with inhibitor 8-azaxanthine | ||||||
Components | Uric acid oxidaseUrate oxidase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Urate Oxidase / Urate Oxidase; / Roll / Alpha Beta / 8-AZAXANTHINE Function and homology information | ||||||
Biological species | Arthrobacter globiformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Hossain, M.T. / Suzuki, K. / Yamamoto, T. / Imamura, S. / Sekiguchi, T. / Takenaka, A. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Uricase from Arthrobacter Globiformis Complexed with an inhibitor 8-Azaxanthine Authors: Hossain, M.T. / Juan, E.C.M. / Suzuki, K. / Yamamoto, T. / Imamura, S. / Sekiguchi, T. / Takenaka, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vay.cif.gz | 468.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vay.ent.gz | 386.4 KB | Display | PDB format |
PDBx/mmJSON format | 1vay.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/1vay ftp://data.pdbj.org/pub/pdb/validation_reports/va/1vay | HTTPS FTP |
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-Related structure data
Related structure data | 1uox 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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2 |
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Unit cell |
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Details | The biological assembly is a tetramer |
-Components
#1: Protein | Mass: 32458.027 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Arthrobacter globiformis (bacteria) / References: factor-independent urate hydroxylase #2: Chemical | ChemComp-AZA / #3: Water | ChemComp-HOH / | |
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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: 2.79 Å3/Da / Density % sol: 55.84 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 9 Details: PEG 8000, Lithium sulphate, pH 9.0, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 13, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→20 Å / Num. all: 739628 / Num. obs: 132537 / % possible obs: 97.4 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.067 |
Reflection shell | Resolution: 2.24→2.32 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.237 / % possible all: 87.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UOX 1uox Resolution: 2.24→20 Å / Cross valid method: THROUGHOUT / σ(F): 3
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Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.24→2.32 Å / Rfactor Rfree error: 0.009
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