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- PDB-4k6o: 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: 4k6o | ||||||
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Title | X-ray structure uridine phosphorylase from Vibrio cholerae in complex with 6-methyluracil at 1.17 A resolution | ||||||
![]() | Uridine phosphorylase | ||||||
![]() | TRANSFERASE / Rossmann Fold | ||||||
Function / homology | ![]() uridine catabolic process / uridine phosphorylase / nucleotide catabolic process / uridine phosphorylase activity / UMP salvage / purine nucleoside catabolic process / purine-nucleoside phosphorylase activity / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Prokofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M. | ||||||
![]() | ![]() Title: Crystallization and preliminary X-ray study of Vibrio cholerae uridine phosphorylase in complex with 6-methyluracil. Authors: Prokofev, I.I. / Lashkov, A.A. / Gabdulkhakov, A.G. / Dontsova, M.V. / Seregina, T.A. / Mironov, A.S. / 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 | ![]() | 1005.1 KB | Display | ![]() |
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PDB format | ![]() | 850.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ip0S 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.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 9 types, 2536 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/6MU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/6MU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-6MU / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-EOH / #8: Chemical | ChemComp-TRS / #9: Chemical | ChemComp-GOL / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.01 % |
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Crystal grow | Temperature: 286 K / pH: 8.5 Details: PEG4000, 0.1M TRIS-HCl, 0.2M MgCl2x6H2O, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 286K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.826 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→80.56 Å / Num. obs: 449315 / % possible obs: 90.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.83 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 11.95 |
Reflection shell | Resolution: 1.17→1.2 Å / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 3.23 / % possible all: 55.3 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4IP0 Resolution: 1.17→40.28 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.07 / σ(F): 1.36 / Phase error: 10.15 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.17→40.28 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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