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Yorodumi- PDB-4u2k: X-ray structure uridine phosphorylase from Vibrio cholerae in com... -
+Open data
-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 | ||||||
Components | Uridine phosphorylase | ||||||
Keywords | TRANSFERASE / Rossmann Fold | ||||||
Function / homology | Function and homology information uridine catabolic process / uridine phosphorylase / nucleotide catabolic process / UMP salvage / uridine phosphorylase activity / purine nucleoside catabolic process / purine-nucleoside phosphorylase activity / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.13 Å | ||||||
Authors | Prokofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M. | ||||||
Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u2k.cif.gz | 299.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u2k.ent.gz | 242.6 KB | Display | PDB format |
PDBx/mmJSON format | 4u2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/4u2k ftp://data.pdbj.org/pub/pdb/validation_reports/u2/4u2k | HTTPS FTP |
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-Related structure data
Related structure data | 4g8jS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Vibrio cholerae (bacteria) Gene: udp, DN30_1909, VC39_02535, VC78_02550, VS27_10630, WG08_05660 Production host: Escherichia coli (E. coli) / References: UniProt: Q9K4U1, uridine phosphorylase |
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-Non-polymers , 7 types, 607 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.000039 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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