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- PDB-4lzw: X-ray structure uridine phosphorylase from Vibrio cholerae in com... -
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Basic information
Entry | Database: PDB / ID: 4lzw | ||||||
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Title | X-ray structure uridine phosphorylase from Vibrio cholerae in complex with thymidine at 1.29 A resolution | ||||||
![]() | Uridine phosphorylase | ||||||
![]() | TRANSFERASE / Rossmann Fold / cytoplasmic | ||||||
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. | ||||||
![]() | ![]() Title: X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases Authors: Prokofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Balaev, V.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 | ![]() | 679.2 KB | Display | ![]() |
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PDB format | ![]() | 558.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 514.8 KB | Display | ![]() |
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Full document | ![]() | 538 KB | Display | |
Data in XML | ![]() | 79.2 KB | Display | |
Data in CIF | ![]() | 119.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ip0C ![]() 5c80C ![]() 4g8jS S: Starting model for refinement C: citing same article ( |
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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 , 7 types, 2000 molecules ![](data/chem/img/THM.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-THM / #3: Chemical | ChemComp-EOH / #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.8 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M MgCl2.6H2O, 15%(w/v) polyethylene glycol (PEG) 4000 in 0.1 M Tris HCl, 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: MAR CCD 165 mm / Detector: CCD / Date: May 9, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.29→29.65 Å / Num. all: 345305 / Num. obs: 342543 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.592 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 9.29 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4G8J Resolution: 1.29→19.89 Å / Occupancy max: 1 / Occupancy min: 0.06 / SU ML: 0.16 / σ(F): 2 / Phase error: 17.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.105 Å2 / ksol: 0.395 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 45.34 Å2 / Biso mean: 11.5438 Å2 / Biso min: 0.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.29→19.89 Å
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Refine LS restraints |
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LS refinement shell |
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