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- PDB-6rca: X-ray structure uridine phosphorylase from Vibrio cholerae in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rca | |||||||||
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Title | X-ray structure uridine phosphorylase from Vibrio cholerae in complex with 2.2'-anhydrouridine at 1.34 A | |||||||||
![]() | Uridine phosphorylase | |||||||||
![]() | TRANSFERASE / Rossmann Fold | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Prokofev, I.I. / Eistrikh-Geller, P.A. / Balaev, V.V. / Gabdoulkhakov, A.G. / Betzel, C. / Lashkov, A.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: X-Ray Structure and Molecular Dynamics Study of Uridine Phosphorylase from Vibrio cholerae in Complex with 2,2'-Anhydrouridine Authors: Eistrikh-Geller, P.A. / Rubinsky, S.V. / Prokofev, I.I. / Gabdoulkhakov, A.G. / Mironov, A.S. / Lashkov, A.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 719 KB | Display | ![]() |
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PDB format | ![]() | 593.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 521.1 KB | Display | ![]() |
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Full document | ![]() | 549.8 KB | Display | |
Data in XML | ![]() | 81.5 KB | Display | |
Data in CIF | ![]() | 122.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4k6oS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() 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: ![]() ![]() |
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-Non-polymers , 7 types, 1996 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/BJE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BJE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-BJE / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-MG / | #7: Chemical | ChemComp-EDO / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.88 % |
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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, pH 8.5, 0.2 M 2,2'-anhydrouridine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.34→44.596 Å / Num. obs: 329624 / % possible obs: 99.7 % / Redundancy: 10.281 % / Biso Wilson estimate: 16.605 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.139 / Rrim(I) all: 0.147 / Χ2: 1.084 / Net I/σ(I): 11.52 / Num. measured all: 3388833 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4K6O Resolution: 1.345→44.596 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 19.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.42 Å2 / Biso mean: 17.1182 Å2 / Biso min: 2.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.345→44.596 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25
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