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- PDB-1ryz: Uridine Phosphorylase from Salmonella typhimurium. Crystal Struct... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ryz | ||||||
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Title | Uridine Phosphorylase from Salmonella typhimurium. Crystal Structure at 2.9 A Resolution | ||||||
![]() | Uridine phosphorylase | ||||||
![]() | TRANSFERASE / uridine phosphorylase / nucleoside phosphorylase | ||||||
Function / homology | ![]() nucleoside catabolic process / uridine phosphorylase / nucleotide catabolic process / uridine phosphorylase activity / UMP salvage / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dontsova, M.V. / Gabdoulkhakov, A.G. / Lyashenko, A.V. / Nikonov, S.V. / Ealick, S.E. / Mikhailov, A.M. | ||||||
![]() | ![]() Title: Structure-functions studies of uridine phosphorylase from Salmonella typhimurium Authors: Dontsova, M.V. / Gabdoulkhakov, A.G. / Lyashenko, A.V. / Nikonov, S.V. / Ealick, S.E. / Mikhailov, A.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 | ![]() | 276.2 KB | Display | ![]() |
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PDB format | ![]() | 223.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1k3fS 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27169.092 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38.98 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M Na Acetate trihydrate, 10% PEG 8000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 2003 / Details: Capillary optics |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. all: 75053 / Num. obs: 26462 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.84 % / Biso Wilson estimate: -0.2 Å2 / Rmerge(I) obs: 0.154 / Rsym value: 0.177 / Net I/σ(I): 6.89 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 2.79 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 3.05 / Num. unique all: 1074 / Rsym value: 0.333 / % possible all: 75.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1K3F Resolution: 2.9→29.46 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 3363606.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.0393 Å2 / ksol: 0.301264 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→29.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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