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- PDB-7q1j: Hybrid form of uridine phosphorylase from E. coli and Salmonella ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7q1j | ||||||
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Title | Hybrid form of uridine phosphorylase from E. coli and Salmonella typhimurium in the presence PEG | ||||||
![]() | Uridine phosphorylase | ||||||
![]() | TRANSFERASE / uridine phosphorylase / hybrid enzyme | ||||||
Function / homology | ![]() nucleoside catabolic process / uridine phosphorylase / nucleotide catabolic process / UMP salvage / uridine phosphorylase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Safonova, T. / Polyakov, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Hybrid form of uridine phosphorylase from E. coli and Salmonella typhimurium in the presence PEG Authors: Polyakov, K. / Safonova, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 23.8 KB | Display | |
Data in CIF | ![]() | 34 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4r2xS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 26882.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-K / | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Potassium citrate tribasic monohydrate, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8025 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→30 Å / Num. obs: 42058 / % possible obs: 99.5 % / Redundancy: 3.82 % / CC1/2: 1 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.71→1.75 Å / Num. unique obs: 3091 / CC1/2: 0.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4R2X Resolution: 1.71→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.261 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / ESU R: 0.148 / ESU R Free: 0.157
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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 PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.903 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→30 Å
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Refine LS restraints |
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LS refinement shell |
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