+Open data
-Basic information
Entry | Database: PDB / ID: 7q31 | ||||||
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Title | Mutant D24G of uridine phosphorylase from E. coli | ||||||
Components | Uridine phosphorylase | ||||||
Keywords | TRANSFERASE / uridine phosphorylase / mutant enzyme | ||||||
Function / homology | Function and homology information uridine phosphorylase / nucleotide catabolic process / UMP salvage / uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / potassium ion binding / DNA damage response / protein-containing complex ...uridine phosphorylase / nucleotide catabolic process / UMP salvage / uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / potassium ion binding / DNA damage response / protein-containing complex / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Safonova, T. / Polyakov, K. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: To Be Published Title: Mutant D24G of uridine phosphorylase from E. coli Authors: Polyakov, K. / Safonova, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q31.cif.gz | 118.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q31.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7q31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q31_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 7q31_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 7q31_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 7q31_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/7q31 ftp://data.pdbj.org/pub/pdb/validation_reports/q3/7q31 | HTTPS FTP |
-Related structure data
Related structure data | 7q32C 4r2xS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 26783.564 Da / Num. of mol.: 2 / Mutation: D24G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: udp, b3831, JW3808 / Production host: Escherichia coli (E. coli) / References: UniProt: P12758, uridine phosphorylase #2: Chemical | ChemComp-K / | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Potassium sulfate, 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: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. obs: 41245 / % possible obs: 97.2 % / Redundancy: 2.6 % / CC1/2: 0.89 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.75→1.8 Å / Num. unique obs: 3140 / CC1/2: 0.67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4R2X Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.437 / SU ML: 0.106 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.128 Details: Hydrogens have been added in their 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: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.153 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→30 Å
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Refine LS restraints |
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LS refinement shell |
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