[English] 日本語
Yorodumi- PDB-4k6o: X-ray structure uridine phosphorylase from Vibrio cholerae in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k6o | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure uridine phosphorylase from Vibrio cholerae in complex with 6-methyluracil at 1.17 A resolution | ||||||
Components | Uridine phosphorylase | ||||||
Keywords | TRANSFERASE / Rossmann Fold | ||||||
Function / homology | Function and homology information uridine phosphorylase / nucleotide catabolic process / uridine catabolic process / UMP salvage / 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: 1.17 Å | ||||||
Authors | Prokofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2014 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4k6o.cif.gz | 1005.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4k6o.ent.gz | 850.4 KB | Display | PDB format |
PDBx/mmJSON format | 4k6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k6o_validation.pdf.gz | 538.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4k6o_full_validation.pdf.gz | 558.3 KB | Display | |
Data in XML | 4k6o_validation.xml.gz | 85.2 KB | Display | |
Data in CIF | 4k6o_validation.cif.gz | 133.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/4k6o ftp://data.pdbj.org/pub/pdb/validation_reports/k6/4k6o | HTTPS FTP |
-Related structure data
Related structure data | 4ip0S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 / Plasmid: pMZ21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K4U1, uridine phosphorylase |
---|
-Non-polymers , 9 types, 2536 molecules
#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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.01 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.826 Å |
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: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
|