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Yorodumi- PDB-4g8j: X-ray Structure of Uridine Phosphorylease from Vibrio cholerae Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g8j | ||||||
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Title | X-ray Structure of Uridine Phosphorylease from Vibrio cholerae Complexed with Thymidine at 2.12 A Resolution | ||||||
Components | Uridine phosphorylase | ||||||
Keywords | TRANSFERASE / Rossmann Fold / alpha-beta-alpha sandwich / Nucleoside and phosphate binding / Phosphorylation / Cytosol | ||||||
Function / homology | Function and homology information 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 | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.119 Å | ||||||
Authors | Lashkov, A.A. / Gabdoulkhakov, A.G. / Prokofev, I.I. / Sotnichenko, S.E. / Betzel, C. / Mikhailov, A.M. | ||||||
Citation | Journal: To be Published Title: X-ray structure of uridine phosphorylease from Vibrio cholerae complexed with thymidine Authors: Lashkov, A.A. / Gabdoulkhakov, A.G. / Prokofev, I.I. / Sotnichenko, S.E. / 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 | 4g8j.cif.gz | 320.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g8j.ent.gz | 255.3 KB | Display | PDB format |
PDBx/mmJSON format | 4g8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4g8j_validation.pdf.gz | 501.6 KB | Display | wwPDB validaton report |
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Full document | 4g8j_full_validation.pdf.gz | 518.7 KB | Display | |
Data in XML | 4g8j_validation.xml.gz | 68.4 KB | Display | |
Data in CIF | 4g8j_validation.cif.gz | 97.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/4g8j ftp://data.pdbj.org/pub/pdb/validation_reports/g8/4g8j | HTTPS FTP |
-Related structure data
Related structure data | 3o6vS 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) / Strain: 569B / Gene: udp / Plasmid: pMZ21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K4U1, uridine phosphorylase |
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-Non-polymers , 6 types, 1335 molecules
#2: Chemical | ChemComp-THM / #3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EDO / #7: 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: 2.15 Å3/Da / Density % sol: 42.91 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Magnesium chloride hexahydrate, TRIS hydrochloride, PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.801 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 14, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.801 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.119→79.611 Å / Num. all: 78327 / Num. obs: 78327 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 14.25 Å2 / Rsym value: 0.082 / Net I/σ(I): 22.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3O6V Resolution: 2.119→11.988 Å / Occupancy max: 1 / Occupancy min: 0.23 / FOM work R set: 0.8901 / SU ML: 0.21 / σ(F): 0 / Phase error: 18.37 / 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: 80.7 Å2 / Biso mean: 17.1027 Å2 / Biso min: 4.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.119→11.988 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: 28
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