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Yorodumi- PDB-5miw: X-ray structure uridine phosphorylase from Vibrio cholerae in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5miw | ||||||
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Title | X-ray structure uridine phosphorylase from Vibrio cholerae in complex with uracil at 1.28 A. | ||||||
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: 1.28 Å | ||||||
Authors | Prokofev, I.I. / Lashkov, A.A. / Balaev, V.V. / 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 uracil at 1.28 A. Authors: Prokofev, I.I. / Lashkov, A.A. / Balaev, V.V. / 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 | 5miw.cif.gz | 712 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5miw.ent.gz | 596.7 KB | Display | PDB format |
PDBx/mmJSON format | 5miw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/5miw ftp://data.pdbj.org/pub/pdb/validation_reports/mi/5miw | HTTPS FTP |
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-Related structure data
Related structure data | 4oehS 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, udp_1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K4U1, uridine phosphorylase |
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-Non-polymers , 7 types, 1927 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-URA / #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | #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: 2.27 Å3/Da / Density % sol: 45.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG4000, 0.1M CHES, 0.2M MgCl2x6H2O |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.896 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.896 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→32.03 Å / Num. obs: 345622 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 3.45 % / Biso Wilson estimate: 9.05 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.131 / Χ2: 0.913 / Net I/σ(I): 10.5 / Num. measured all: 1344228 |
Reflection shell | Resolution: 1.28→1.36 Å / Redundancy: 3.826 % / Rmerge(I) obs: 0.888 / Mean I/σ(I) obs: 1.79 / Num. measured obs: 52031 / Num. possible: 13760 / Num. unique obs: 13600 / CC1/2: 0.998 / Rrim(I) all: 0.035 / % possible all: 82.9 |
-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.53
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OEH Resolution: 1.28→32.03 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 17.76
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.17 Å2 / Biso mean: 16.65 Å2 / Biso min: 2.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.28→32.03 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26
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