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Yorodumi- PDB-4oby: Crystal Structure of E.coli Arginyl-tRNA Synthetase and Ligand Bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oby | ||||||
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Title | Crystal Structure of E.coli Arginyl-tRNA Synthetase and Ligand Binding Studies Revealed Key Residues in Arginine Recognition | ||||||
Components | Arginine--tRNA ligase | ||||||
Keywords | LIGASE | ||||||
Function / homology | Function and homology information arginine-tRNA ligase / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.574 Å | ||||||
Authors | Bi, K. / Zheng, Y. / Dong, J. / Gao, F. / Wang, J. / Wang, Y. / Gong, W. | ||||||
Citation | Journal: Protein Cell / Year: 2014 Title: Crystal structure of E. coli arginyl-tRNA synthetase and ligand binding studies revealed key residues in arginine recognition. Authors: Bi, K. / Zheng, Y. / Gao, F. / Dong, J. / Wang, J. / Wang, Y. / Gong, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oby.cif.gz | 228.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oby.ent.gz | 183.8 KB | Display | PDB format |
PDBx/mmJSON format | 4oby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/4oby ftp://data.pdbj.org/pub/pdb/validation_reports/ob/4oby | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 64848.887 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: argS, b1876, JW1865 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11875, arginine-tRNA ligase |
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#2: Chemical | ChemComp-ARG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.41 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 10mg/ml protein sample in 20 mM Tris, pH 7.5, reservior solution - 50mM HEPES (pH 7.2), 100mM sodium acetate, 22% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 20541 / % possible obs: 99.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 |
Reflection shell | Resolution: 2.6→50 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BS2 as ensemble 1 and 3GDZ as ensemble 2 Resolution: 2.574→35.906 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 33.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.574→35.906 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 27.0681 Å / Origin y: 66.6646 Å / Origin z: 20.3726 Å
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Refinement TLS group | Selection details: all |