[English] 日本語
Yorodumi- PDB-3e9h: Lysyl-tRNA synthetase from Bacillus stearothermophilus complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e9h | ||||||
---|---|---|---|---|---|---|---|
Title | Lysyl-tRNA synthetase from Bacillus stearothermophilus complexed with L-Lysylsulfamoyl adenosine | ||||||
Components | Lysyl-tRNA synthetase | ||||||
Keywords | LIGASE / aminoacyl tRNA synthetase / PROTEIN BIOSYNTHESIS / Aminoacyl-tRNA synthetase / ATP-binding / Cytoplasm / Magnesium / Metal-binding / Nucleotide-binding | ||||||
Function / homology | Function and homology information lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / transferase activity / nucleic acid binding / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Sakurama, H. / Takita, T. / Mikami, B. / Itoh, T. / Yasukawa, K. / Inouye, K. | ||||||
Citation | Journal: J.Biochem. / Year: 2009 Title: Two crystal structures of lysyl-tRNA synthetase from Bacillus stearothermophilus in complex with lysyladenylate-like compounds: insights into the irreversible formation of the enzyme-bound ...Title: Two crystal structures of lysyl-tRNA synthetase from Bacillus stearothermophilus in complex with lysyladenylate-like compounds: insights into the irreversible formation of the enzyme-bound adenylate of L-lysine hydroxamate Authors: Sakurama, H. / Takita, T. / Mikami, B. / Itoh, T. / Yasukawa, K. / Inouye, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3e9h.cif.gz | 406.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3e9h.ent.gz | 330.6 KB | Display | PDB format |
PDBx/mmJSON format | 3e9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/3e9h ftp://data.pdbj.org/pub/pdb/validation_reports/e9/3e9h | HTTPS FTP |
---|
-Related structure data
Related structure data | 3e9iC 1bbuS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 57359.305 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus stearothermophilus (bacteria) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RHV9, lysine-tRNA ligase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-KAA / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.52 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 18% PEG4000, 0.2M PIPES, 1.0M LiCl, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 27, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 111633 / % possible obs: 90.2 % / Biso Wilson estimate: 15 Å2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BBU Resolution: 2.1→14.97 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3069815.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.0297 Å2 / ksol: 0.36261 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→14.97 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|