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Yorodumi- PDB-6eyp: X-ray structure of the unliganded uridine phosphorylase from Vibr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eyp | ||||||
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Title | X-ray structure of the unliganded uridine phosphorylase from Vibrio cholerae at 1.22A | ||||||
Components | Uridine phosphorylase | ||||||
Keywords | TRANSFERASE / Rossmann Fold | ||||||
Function / homology | Function and homology information uridine phosphorylase / nucleotide catabolic process / uridine phosphorylase activity / UMP salvage / nucleoside catabolic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.22 Å | ||||||
Authors | Prokofev, I.I. / Balaev, V.V. / Gabdoulkhakov, A.G. / Betzel, C. / Lashkov, A.A. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: To Be Published Title: X-ray structure of the unliganded uridine phosphorylase from Vibrio cholerae at 1.22A Authors: Prokofev, I.I. / Balaev, V.V. / Gabdoulkhakov, A.G. / Betzel, C. / Lashkov, A.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eyp.cif.gz | 696.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eyp.ent.gz | 586.7 KB | Display | PDB format |
PDBx/mmJSON format | 6eyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/6eyp ftp://data.pdbj.org/pub/pdb/validation_reports/ey/6eyp | 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
#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, B2J67_05455, B2J68_05210, B2J71_05165, BFX32_04820, BTY66_05555, CEF09_03900, DN30_1909, EN12_05055, ERS013138_02408, ERS013140_00580, ERS013186_00327, ERS013199_00063, ERS013201_ ...Gene: udp, udp_1, B2J67_05455, B2J68_05210, B2J71_05165, BFX32_04820, BTY66_05555, CEF09_03900, DN30_1909, EN12_05055, ERS013138_02408, ERS013140_00580, ERS013186_00327, ERS013199_00063, ERS013201_00032, ERS013202_00369, ERS013206_00377 Production host: Escherichia coli (E. coli) / References: UniProt: Q9K4U1, uridine phosphorylase #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-MG / | #5: 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: 42.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0,2 M MgCl2,6H2O, 15%(w/v) PEG 4000, 0,1 M TRIS -HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.886 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.886 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→26.48 Å / Num. obs: 399225 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.05 % / Biso Wilson estimate: 9.73 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.131 / Χ2: 1.156 / Net I/σ(I): 10.75 / Num. measured all: 4015025 |
Reflection shell | Resolution: 1.22→1.3 Å / Redundancy: 9.59 % / Rmerge(I) obs: 1.065 / Mean I/σ(I) obs: 1.88 / Num. measured obs: 147782 / Num. possible: 14978 / Num. unique obs: 63823 / CC1/2: 0.998 / Rrim(I) all: 1.125 / % possible all: 98.6 |
-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: 4OEH Resolution: 1.22→26.48 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 18.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.39 Å2 / Biso mean: 18.18 Å2 / Biso min: 1.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.22→26.48 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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