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Yorodumi- PDB-2oxf: X-ray structure of the unliganded uridine phosphorylase from Salm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oxf | ||||||
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Title | X-ray structure of the unliganded uridine phosphorylase from Salmonella typhimurium in homodimeric form at 1.76A resolution | ||||||
Components | Uridine phosphorylase | ||||||
Keywords | TRANSFERASE / NUCLEOSIDE PHOSPHORYLASE | ||||||
Function / homology | Function and homology information uridine phosphorylase / nucleotide catabolic process / uridine phosphorylase activity / UMP salvage / nucleoside catabolic process / cytosol Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Timofeev, V.I. / Pavlyk, B.P. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Mikhailov, A.M. | ||||||
Citation | Journal: To be Published Title: X-ray structure of the unliganded uridine phosphorylase from Salmonella typhimurium in homodimeric form at 1.76A resolution Authors: Timofeev, V.I. / Pavlyk, B.P. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Mikhailov, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oxf.cif.gz | 105.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oxf.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 2oxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/2oxf ftp://data.pdbj.org/pub/pdb/validation_reports/ox/2oxf | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a hexamer generated from the dimer, which presented in the asymmetric unit |
-Components
#1: Protein | Mass: 26821.637 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: UDP / Plasmid: PBLUESCRIPT IISK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P0A1F6, uridine phosphorylase #2: Chemical | ChemComp-GOL / | #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: 1.95 Å3/Da / Density % sol: 37 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.76→150.86 Å / Num. obs: 39165 |
-Processing
Software | Name: PHENIX / Classification: refinement | ||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.76→8 Å
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Refine LS restraints |
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