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- PDB-4r2w: X-ray structure of uridine phosphorylase from Shewanella oneidens... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4r2w | |||||||||
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Title | X-ray structure of uridine phosphorylase from Shewanella oneidensis MR-1 in complex with uridine at 1.6 A resolution | |||||||||
![]() | Uridine phosphorylase | |||||||||
![]() | TRANSFERASE / Uridine phosphorylase / Uridine Binding | |||||||||
Function / homology | ![]() nucleoside catabolic process / uridine phosphorylase / nucleotide catabolic process / uridine phosphorylase activity / UMP salvage / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Safonova, T.N. / Mordkovich, N.N. / Manuvera, V.A. / Veiko, V.P. / Popov, V.O. / Polyakov, K.P. | |||||||||
![]() | ![]() 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 | ![]() | 287 KB | Display | ![]() |
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PDB format | ![]() | 231.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4r2xC ![]() 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-GOL / #4: Chemical | ChemComp-URI / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.75M ammonium sulfate, 0.075M Bis-Tris, pH 5.5, 0.75% (w/v) PEG 3350, 25% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP , temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 8, 2009 | ||||||||||||||||||||
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength | Wavelength: 0.812 Å / Relative weight: 1 | ||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.6→79.62 Å / Num. all: 205488 / Num. obs: 171553 / % possible obs: 77.3 % / Observed criterion σ(I): 1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1rxy Resolution: 1.6→19.49 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.421 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: refinement against detwinned data
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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: 17.451 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→19.49 Å
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Refine LS restraints |
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