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- PDB-3p0e: Structure of hUPP2 in an active conformation with bound 5-benzyla... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3p0e | ||||||
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Title | Structure of hUPP2 in an active conformation with bound 5-benzylacyclouridine | ||||||
![]() | Uridine phosphorylase 2 | ||||||
![]() | TRANSFERASE / uridine phosphorylase | ||||||
Function / homology | ![]() type III intermediate filament / uridine metabolic process / deoxyuridine phosphorylase activity / dCMP catabolic process / Pyrimidine catabolism / Pyrimidine salvage / uridine phosphorylase / uridine catabolic process / UMP salvage / nucleoside metabolic process ...type III intermediate filament / uridine metabolic process / deoxyuridine phosphorylase activity / dCMP catabolic process / Pyrimidine catabolism / Pyrimidine salvage / uridine phosphorylase / uridine catabolic process / UMP salvage / nucleoside metabolic process / uridine phosphorylase activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Roosild, T.P. / Castronovo, S. / Villoso, A. | ||||||
![]() | ![]() Title: A novel structural mechanism for redox regulation of uridine phosphorylase 2 activity. Authors: Roosild, T.P. / Castronovo, S. / Villoso, A. / Ziemba, A. / Pizzorno, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 343.8 KB | Display | ![]() |
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PDB format | ![]() | 282.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 63.3 KB | Display | |
Data in CIF | ![]() | 86.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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: 33232.609 Da / Num. of mol.: 6 / Fragment: UNP residues 21-314 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-BAU / #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.83 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 2.0M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 134252 / % possible obs: 92.4 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.153 / Χ2: 1.056 / Net I/σ(I): 9.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.16 Å2 / Biso mean: 33.1254 Å2 / Biso min: 15.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2→35.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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