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Yorodumi- PDB-2yzc: Crystal structure of uricase from Arthrobacter globiformis in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yzc | ||||||
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Title | Crystal structure of uricase from Arthrobacter globiformis in complex with allantoate | ||||||
Components | Uricase | ||||||
Keywords | OXIDOREDUCTASE / uricase / allantoate | ||||||
Function / homology | Function and homology information purine nucleobase catabolic process / urate oxidase activity / factor-independent urate hydroxylase / urate catabolic process / peroxisome Similarity search - Function | ||||||
Biological species | Arthrobacter globiformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Juan, E.C.M. / Hossain, M.T. / Hoque, M.M. / Suzuki, K. / Sekiguchi, T. / Takenaka, A. | ||||||
Citation | Journal: To be Published Title: Trapping of the uric acid substrate in the crystal structure of urate oxidase from Arthrobacter globiformis Authors: Juan, E.C.M. / Hossain, M.T. / Hoque, M.M. / Yamamoto, T. / Imamura, S. / Suzuki, K. / 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 | 2yzc.cif.gz | 493.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yzc.ent.gz | 403.8 KB | Display | PDB format |
PDBx/mmJSON format | 2yzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/2yzc ftp://data.pdbj.org/pub/pdb/validation_reports/yz/2yzc | HTTPS FTP |
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-Related structure data
Related structure data | 2yzbC 2yzdC 2yzeC 1uox C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33900.629 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Arthrobacter globiformis (bacteria) References: UniProt: D0VWQ1*PLUS, factor-independent urate hydroxylase #2: Chemical | ChemComp-1AL / #3: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE DATABASE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN UNP. IT WILL BE SUBMITTED TO UNP ...THE SEQUENCE DATABASE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN UNP. IT WILL BE SUBMITTED TO UNP DATABASE SOON. | |
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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: 2.76 Å3/Da / Density % sol: 55.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: PEG8000, lithium sulfate, sodium borate buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: Oct 3, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→50 Å / Num. obs: 231814 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.076 |
Reflection shell | Resolution: 1.88→1.95 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.236 / % possible all: 83.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1uox 1uox Resolution: 1.88→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.463 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.118 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.551 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.883→1.931 Å / Total num. of bins used: 20 /
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