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- PDB-2prz: S. cerevisiae orotate phosphoribosyltransferase complexed with OMP -
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Open data
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Basic information
Entry | Database: PDB / ID: 2prz | ||||||
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Title | S. cerevisiae orotate phosphoribosyltransferase complexed with OMP | ||||||
![]() | Orotate phosphoribosyltransferase 1 | ||||||
![]() | TRANSFERASE / ALPHA BETA / OPRTase-OMP complex | ||||||
Function / homology | ![]() pyrimidine ribonucleoside biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleotide biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gonzalez-Segura, L. / Hurley, T.D. / McClard, R.W. | ||||||
![]() | ![]() Title: Ternary complex formation and induced asymmetry in orotate phosphoribosyltransferase. Authors: Gonzalez-Segura, L. / Witte, J.F. / McClard, R.W. / Hurley, T.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183.5 KB | Display | ![]() |
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PDB format | ![]() | 145.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 38.3 KB | Display | |
Data in CIF | ![]() | 52.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2prySC ![]() 2ps1C S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
#1: Protein | Mass: 24689.439 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: URA5, PYR5 / Plasmid: pREJ2 / Production host: ![]() ![]() References: UniProt: P13298, orotate phosphoribosyltransferase #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-OMP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.31 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 28% PEG 6000, 0.08M magnesium acetate, 0.1M Tris HCl, 2.5mM magnesium chloride, 5.0mM OMP, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→50 Å / Num. all: 77826 / Num. obs: 74091 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.2 / Redundancy: 5.1 % / Biso Wilson estimate: 27.025 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.048 / Χ2: 1.044 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.89→1.96 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.4 / Num. unique all: 5115 / Rsym value: 0.376 / Χ2: 0.86 / % possible all: 66.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PRY (S. cerevisiae OPRTase apo form) Resolution: 1.895→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.182 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.187 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.996 Å2
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Refinement step | Cycle: LAST / Resolution: 1.895→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.895→1.944 Å / Total num. of bins used: 20
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