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- PDB-4r2x: Unique conformation of uridine and asymmetry of the hexameric mol... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4r2x | |||||||||
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Title | Unique conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis uridine phosphorylase in the free form and in complex with uridine | |||||||||
![]() | uridine phosphorylase | |||||||||
![]() | TRANSFERASE / uridine phosphorylase | |||||||||
Function / homology | ![]() uridine phosphorylase / nucleotide catabolic process / UMP salvage / uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Safonova, T.N. / Mordkovich, N.N. / Manuvera, V.A. / Veiko, V.P. / Popov, V.O. / Polyakov, K.M. | |||||||||
![]() | ![]() Title: High-syn conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis MR-1 uridine phosphorylase in the free form and in complex with uridine. Authors: Safonova, T.N. / Mikhailov, S.N. / Veiko, V.P. / Mordkovich, N.N. / Manuvera, V.A. / Alekseev, C.S. / Kovalchuk, M.V. / Popov, V.O. / Polyakov, K.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 805.2 KB | Display | ![]() |
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PDB format | ![]() | 677.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 507.1 KB | Display | ![]() |
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Full document | ![]() | 521.9 KB | Display | |
Data in XML | ![]() | 63.4 KB | Display | |
Data in CIF | ![]() | 92.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4r2wC ![]() 1rxyS C: citing same article ( 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
#1: Protein | Mass: 26877.680 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.06 % |
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Crystal grow | Temperature: 293 K / pH: 5.5 Details: 0.75M ammonium sulfate, 0.1M Bis-Tris, pH 5.5, 0.75% (w/v) PEG 3350, 25% (v/v) glycerol, temperature 293K, FREE INTERFACE DIFFUSION, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 20, 2011 | ||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 | ||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 0.93→79.35 Å / Num. obs: 883288 / % possible obs: 93.5 % / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.126 / Rsym value: 0.87 / Net I/σ(I): 12.2 | ||||||||||||||||||||
Reflection shell | Resolution: 0.95→1 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.708 / % possible all: 93.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RXY Resolution: 0.93→29.66 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.423 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.004 / ESU R Free: 0.004 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.86 Å2
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Refinement step | Cycle: LAST / Resolution: 0.93→29.66 Å
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Refine LS restraints |
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