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- PDB-4u2k: 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: 4u2k | ||||||
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Title | X-ray structure uridine phosphorylase from Vibrio cholerae in complex with anticancer compound at 2.13 A resolution | ||||||
![]() | 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. | ||||||
![]() | ![]() Title: X-ray structure uridine phosphorylase from Vibrio cholerae in complex with new anticancer compound at 1.17 A resolution 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 | ![]() | 299.5 KB | Display | ![]() |
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PDB format | ![]() | 242.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 549.9 KB | Display | ![]() |
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Full document | ![]() | 592.2 KB | Display | |
Data in XML | ![]() | 63.2 KB | Display | |
Data in CIF | ![]() | 87.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4g8jS 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, DN30_1909, VC39_02535, VC78_02550, VS27_10630, WG08_05660 Production host: ![]() ![]() |
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-Non-polymers , 7 types, 607 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/4WR.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/M5F.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/4WR.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/M5F.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Chemical | #7: Chemical | ChemComp-TRS / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting 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: Dec 5, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.000039 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.13→38.003 Å / Num. all: 71570 / Num. obs: 71570 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 20.22 Å2 / Rpim(I) all: 0.036 / Rrim(I) all: 0.115 / Rsym value: 0.109 / Net I/av σ(I): 4.61 / Net I/σ(I): 13.8 / Num. measured all: 708536 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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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: ![]() Starting model: 4G8J Resolution: 2.13→19.771 Å / FOM work R set: 0.7661 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2.12 / Phase error: 30.33 / 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 max: 78.44 Å2 / Biso mean: 23.23 Å2 / Biso min: 4.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.13→19.771 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: 15
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