+Open data
-Basic information
Entry | Database: PDB / ID: 2ehj | ||||||
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Title | Structure of Uracil phosphoribosyl transferase | ||||||
Components | Uracil phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / uracil phosphoribosyl transferase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information uracil salvage / uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / pyrimidine nucleobase metabolic process / UMP salvage / guanosine tetraphosphate binding / GTP binding / magnesium ion binding / identical protein binding / membrane ...uracil salvage / uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / pyrimidine nucleobase metabolic process / UMP salvage / guanosine tetraphosphate binding / GTP binding / magnesium ion binding / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Lokanath, N.K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Structure of Uracil phosphoribosyl transferase Authors: Lokanath, N.K. / Pampa, K.J. / Kamiya, T. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ehj.cif.gz | 168.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ehj.ent.gz | 135.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ehj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ehj_validation.pdf.gz | 472.7 KB | Display | wwPDB validaton report |
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Full document | 2ehj_full_validation.pdf.gz | 497 KB | Display | |
Data in XML | 2ehj_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 2ehj_validation.cif.gz | 45.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/2ehj ftp://data.pdbj.org/pub/pdb/validation_reports/eh/2ehj | HTTPS FTP |
-Related structure data
Related structure data | 1v9sS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 22558.236 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Description: cell-free synthesis / Production host: Escherichia coli (E. coli) References: UniProt: P0A8F0, uracil phosphoribosyltransferase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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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: 3.08 Å3/Da / Density % sol: 60.09 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 0.05M MES, 1.5M NH2SO4, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Nov 4, 2006 / Details: GRAPHITE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→40 Å / Num. all: 28689 / Num. obs: 28400 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1V9S Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.921 / SU B: 22.953 / SU ML: 0.22 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.442 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.382 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.871 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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