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- PDB-5epu: X-ray structure uridine phosphorylase from Vibrio cholerae in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5epu | ||||||
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Title | X-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytosine at 1.06A. | ||||||
![]() | Uridine phosphorylase | ||||||
![]() | TRANSFERASE / Rossmann Fold | ||||||
Function / homology | ![]() uridine phosphorylase / nucleotide catabolic process / UMP salvage / uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Prokofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: X-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytosine at 1.06A. Authors: Prokofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 527.3 KB | Display | ![]() |
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Full document | ![]() | 563 KB | Display | |
Data in XML | ![]() | 85.3 KB | Display | |
Data in CIF | ![]() | 129.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4k6oS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 27108.994 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: udp, udp_1, udp_2, DN30_1909, EN12_05055, ERS013138_02408, ERS013140_00580, ERS013160_01327, ERS013186_00327, ERS013199_00063, ERS013201_00032, ERS013202_00369, ERS013206_00377, ERS013212_00480 Production host: ![]() ![]() |
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-Non-polymers , 8 types, 2148 molecules ![](data/chem/img/CYT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CYT / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG4000, 0.1M TRIS-HCl, 0.2M MgCl2x6H2O |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 16, 2015 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97989 Å / Relative weight: 1 |
Reflection | Resolution: 1.06→46.461 Å / Num. obs: 615831 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 11.28 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 16.26 |
Reflection shell | Resolution: 1.06→1.12 Å / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.54 / Rejects: 0 / % possible all: 83.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4K6O Resolution: 1.06→46.46 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.982 / WRfactor Rfree: 0.1135 / WRfactor Rwork: 0.099 / FOM work R set: 0.9237 / SU B: 0.594 / SU ML: 0.013 / SU R Cruickshank DPI: 0.0215 / SU Rfree: 0.0217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 133.93 Å2 / Biso mean: 11.75 Å2 / Biso min: 2.83 Å2
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Refinement step | Cycle: final / Resolution: 1.06→46.46 Å
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Refine LS restraints |
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