+Open data
-Basic information
Entry | Database: PDB / ID: 3kvr | |||||||||
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Title | Trapping of an oxocarbenium ion intermediate in UP crystals | |||||||||
Components | Uridine phosphorylase | |||||||||
Keywords | TRANSFERASE / Oxocarbenium Ion / Glycal / Pyrimidine Salvage / Uridine Phosphorylase | |||||||||
Function / homology | Function and homology information uridine phosphorylase / nucleotide catabolic process / uridine phosphorylase activity / UMP salvage / nucleoside catabolic process / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Paul, D. / O'Leary, S. / Rajashankar, K. / Bu, W. / Toms, A. / Settembre, E. / Sanders, J. / Begley, T.P. / Ealick, S.E. | |||||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Glycal formation in crystals of uridine phosphorylase. Authors: Paul, D. / O'Leary, S.E. / Rajashankar, K. / Bu, W. / Toms, A. / Settembre, E.C. / Sanders, J.M. / Begley, T.P. / 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 | 3kvr.cif.gz | 125 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kvr.ent.gz | 98.6 KB | Display | PDB format |
PDBx/mmJSON format | 3kvr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/3kvr ftp://data.pdbj.org/pub/pdb/validation_reports/kv/3kvr | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33922.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: UPP1 / Plasmid: XF1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3) / References: UniProt: A5PJH9, uridine phosphorylase #2: Chemical | #3: Chemical | #4: Sugar | #5: 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: 3.24 Å3/Da / Density % sol: 61.99 % |
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Crystal grow | Temperature: 295 K / pH: 6.3 Details: 18% PEG5K MME, 140 mM MgCl2, 100 mM MES, pH 6.3, 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 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 28268 / Biso Wilson estimate: 33.9 Å2 |
Reflection shell | Highest resolution: 2.6 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Highest resolution: 2.6 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 2.57 / σ(F): 0.14 / 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 / Bsol: 29.85 Å2 / ksol: 0.34 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.74 Å2
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Refinement step | Cycle: LAST / Highest resolution: 2.6 Å
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Refine LS restraints |
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LS refinement shell |
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