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- PDB-1j09: Crystal structure of Thermus thermophilus glutamyl-tRNA synthetas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j09 | ||||||
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Title | Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP and Glu | ||||||
![]() | Glutamyl-tRNA synthetase | ||||||
![]() | LIGASE / GluRS-ATP-Glu complex / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | ![]() glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / tRNA binding / zinc ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sekine, S. / Nureki, O. / Dubois, D.Y. / Bernier, S. / Chenevert, R. / Lapointe, J. / Vassylyev, D.G. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding Authors: Sekine, S. / Nureki, O. / Dubois, D.Y. / Bernier, S. / Chenevert, R. / Lapointe, J. / Vassylyev, D.G. / Yokoyama, S. #1: ![]() Title: Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase Authors: Sekine, S. / Nureki, O. / Shimada, A. / Vassylyev, D.G. / Yokoyama, S. #2: ![]() Title: Architectures of class-defining and specific domains of glutamyl-tRNA synthetase Authors: Nureki, O. / Vassylyev, D.G. / Katayanagi, K. / Shimizu, T. / Sekine, S. / Kigawa, T. / Miyazawa, T. / Yokoyama, S. / Morikawa, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.8 KB | Display | ![]() |
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PDB format | ![]() | 88.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 814.5 KB | Display | ![]() |
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Full document | ![]() | 821.4 KB | Display | |
Data in XML | ![]() | 22.7 KB | Display | |
Data in CIF | ![]() | 33.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1n75C ![]() 1n77C ![]() 1n78C ![]() 1glnS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 53988.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GLU / |
#4: Chemical | ChemComp-ATP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.04 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 or 20 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 11, 2001 |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. all: 49026 / Num. obs: 49026 / % possible obs: 91.7 % / Observed criterion σ(I): -1 / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.063 |
Reflection shell | Resolution: 1.8→1.88 Å / Rmerge(I) obs: 0.444 / % possible all: 92.8 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 208385 |
Reflection shell | *PLUS % possible obs: 92.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB 1GLN Resolution: 1.8→37.12 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1790268.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 70.4768 Å2 / ksol: 0.355014 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→37.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.88 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 40 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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