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Yorodumi- PDB-3qpb: Crystal Structure of Streptococcus Pyogenes Uridine Phosphorylase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qpb | |||||||||
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Title | Crystal Structure of Streptococcus Pyogenes Uridine Phosphorylase Reveals a Subclass of the NP-I Superfamily | |||||||||
Components | Uridine phosphorylase | |||||||||
Keywords | TRANSFERASE / hexamer / NP-I superfamily / pyrimidine salvage pathway / uridine phosphorylase / transition state | |||||||||
Function / homology | Function and homology information uridine phosphorylase / nucleotide catabolic process / uridine phosphorylase activity / UMP salvage / nucleoside metabolic process / purine-nucleoside phosphorylase activity / cytoplasm Similarity search - Function | |||||||||
Biological species | Streptococcus pyogenes serotype M6 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | |||||||||
Authors | Tran, T.H. / Christoffersen, S. / Parker, W.B. / Piskur, J. / Serra, I. / Terreni, M. / Ealick, S.E. | |||||||||
Citation | Journal: Biochemistry / Year: 2011 Title: The Crystal Structure of Streptococcus pyogenes Uridine Phosphorylase Reveals a Distinct Subfamily of Nucleoside Phosphorylases. Authors: Tran, T.H. / Christoffersen, S. / Allan, P.W. / Parker, W.B. / Serra, I. / Terreni, M. / Ealick, S.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qpb.cif.gz | 894 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qpb.ent.gz | 733.2 KB | Display | PDB format |
PDBx/mmJSON format | 3qpb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/3qpb ftp://data.pdbj.org/pub/pdb/validation_reports/qp/3qpb | 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 30555.420 Da / Num. of mol.: 18 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes serotype M6 (bacteria) Gene: M6_Spy1599 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5XA29, uridine phosphorylase #2: Sugar | ChemComp-R1P / #3: Chemical | ChemComp-URA / #4: 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: 2.21 Å3/Da / Density % sol: 44.43 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 18% PEG 4000, 16% isopropanol, and 0.1 M sodium citrate pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2008 |
Radiation | Monochromator: CRYO-COOLED SI(111) DOUBLE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→50 Å / Num. obs: 404352 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→50 Å
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Refinement step | Cycle: LAST / Resolution: 1.82→50 Å
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