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Open data
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Basic information
Entry | Database: PDB / ID: 3nbq | ||||||
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Title | Human uridine phosphorylase 1 (hUPP1) with 5-fluorouracil | ||||||
![]() | Uridine phosphorylase 1 | ||||||
![]() | TRANSFERASE / nucleoside phosphorylase / 5-fluorouracil / chemotherapy | ||||||
Function / homology | ![]() deoxyuridine phosphorylase activity / CMP catabolic process / dTMP catabolic process / UMP catabolic process / dCMP catabolic process / thymidine phosphorylase activity / dUMP catabolic process / Pyrimidine catabolism / uridine catabolic process / Pyrimidine salvage ...deoxyuridine phosphorylase activity / CMP catabolic process / dTMP catabolic process / UMP catabolic process / dCMP catabolic process / thymidine phosphorylase activity / dUMP catabolic process / Pyrimidine catabolism / uridine catabolic process / Pyrimidine salvage / uridine phosphorylase / uridine phosphorylase activity / UMP salvage / nucleobase-containing compound metabolic process / cellular response to glucose starvation / nucleoplasm / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Roosild, T.P. | ||||||
![]() | ![]() Title: Active site conformational dynamics in human uridine phosphorylase 1. Authors: Roosild, T.P. / Castronovo, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 232.6 KB | Display | ![]() |
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PDB format | ![]() | 186.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 3 / Auth seq-ID: 78 - 84 / Label seq-ID: 96 - 102
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Components
#1: Protein | Mass: 36050.617 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-URF / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.93 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 17% PEG 3350, 100mM Bis-Tris buffer pH 5.5, 160mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 58528 / % possible obs: 94.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.059 / Χ2: 0.987 / Net I/σ(I): 13.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 77.58 Å2 / Biso mean: 37.233 Å2 / Biso min: 7.85 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→43.44 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.357 Å / Total num. of bins used: 20
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