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Open data
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Basic information
Entry | Database: PDB / ID: 1jii | ||||||
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Title | Crystal structure of S. aureus TyrRS in complex with SB-219383 | ||||||
![]() | tyrosyl-tRNA synthetase | ||||||
![]() | LIGASE / tyrosyl-trna synthetase / staphylococcus aureus / truncation / structure based inhibitor design | ||||||
Function / homology | ![]() tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / RNA binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Qiu, X. / Janson, C.A. / Smith, W.W. / Jarvest, R.L. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.5 KB | Display | ![]() |
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PDB format | ![]() | 50.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456 KB | Display | ![]() |
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Full document | ![]() | 485 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | the biological assembly is a dimer generated from the monomer in ASU and the operation -x,y,-z+1/2 ---- operation 3 |
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Components
#1: Protein | Mass: 47655.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: GenBank: 13701524, UniProt: A6QHR2*PLUS, tyrosine-tRNA ligase |
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#2: Chemical | ChemComp-383 / [ |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.16 % | ||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jun 6, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→27 Å / Num. all: 8608 / Num. obs: 8530 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 3.2→3.24 Å / Redundancy: 4 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 1.9 / % possible all: 99 |
Reflection | *PLUS % possible obs: 99 % / Num. measured all: 31808 |
Reflection shell | *PLUS % possible obs: 99 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: B. stearothermophilus Resolution: 3.2→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 3.2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.269 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.9 |