+Open data
-Basic information
Entry | Database: PDB / ID: 1jil | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of S. aureus TyrRS in complex with SB284485 | ||||||
Components | tyrosyl-tRNA synthetase | ||||||
Keywords | LIGASE / tyrosyl-trna synthetase / staphylococcus aureus / truncation / structure based inhibitor design | ||||||
Function / homology | Function and homology information tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / RNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å | ||||||
Authors | Qiu, X. / Janson, C.A. / Smith, W.W. / Jarvest, R.L. | ||||||
Citation | Journal: Protein Sci. / Year: 2001 Title: Crystal structure of Staphylococcus aureus tyrosyl-tRNA synthetase in complex with a class of potent and specific inhibitors. Authors: Qiu, X. / Janson, C.A. / Smith, W.W. / Green, S.M. / McDevitt, P. / Johanson, K. / Carter, P. / Hibbs, M. / Lewis, C. / Chalker, A. / Fosberry, A. / Lalonde, J. / Berge, J. / Brown, P. / ...Authors: Qiu, X. / Janson, C.A. / Smith, W.W. / Green, S.M. / McDevitt, P. / Johanson, K. / Carter, P. / Hibbs, M. / Lewis, C. / Chalker, A. / Fosberry, A. / Lalonde, J. / Berge, J. / Brown, P. / Houge-Frydrych, C.S. / Jarvest, R.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jil.cif.gz | 84.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jil.ent.gz | 62.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/1jil ftp://data.pdbj.org/pub/pdb/validation_reports/ji/1jil | HTTPS FTP |
---|
-Related structure data
Related structure data | 1jiiC 1jijC 1jikSC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
| ||||||||||||||||||
Details | the biological assembly is a dimer generated from the monomer in ASU and the operation -x+1, 1/2-y, z |
-Components
#1: Protein | Mass: 47655.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Variant: aureus N315 / Production host: Escherichia coli (E. coli) References: GenBank: 13701524, UniProt: A6QHR2*PLUS, tyrosine-tRNA ligase |
---|---|
#2: Chemical | ChemComp-485 / [ |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.6 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.25 Details: PEG 1000, CaCl2, pH 7.25, VAPOR DIFFUSION, SITTING DROP at 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jun 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→45 Å / Num. obs: 23968 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 3.3 / Num. unique all: 838 / % possible all: 69 |
Reflection | *PLUS Lowest resolution: 45 Å / % possible obs: 97 % / Num. measured all: 83183 |
Reflection shell | *PLUS % possible obs: 69 % |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1JIK Resolution: 2.2→45 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→45 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 45 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.183 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|