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Yorodumi- PDB-1n78: Crystal structure of Thermus thermophilus glutamyl-tRNA synthetas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n78 | ||||||
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Title | Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with tRNA(Glu) and glutamol-AMP. | ||||||
Components |
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Keywords | ligase/RNA / ERS/tRNA/GOA / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / ligase-RNA COMPLEX | ||||||
Function / homology | Function and homology information glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / tRNA binding / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Sekine, S. / Nureki, O. / Dubois, D.Y. / Bernier, S. / Chenevert, R. / Lapointe, J. / Vassylyev, D.G. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: EMBO J. / Year: 2003 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: Journal: Nat.Struct.Biol. / Year: 2001 Title: Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase Authors: Sekine, S. / Nureki, O. / Shimada, A. / Vassylyev, D.G. / Yokoyama, S. #2: Journal: Science / Year: 1995 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n78.cif.gz | 300.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n78.ent.gz | 234.2 KB | Display | PDB format |
PDBx/mmJSON format | 1n78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/1n78 ftp://data.pdbj.org/pub/pdb/validation_reports/n7/1n78 | HTTPS FTP |
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-Related structure data
Related structure data | 1j09C 1n75C 1n77C 1g59S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 24105.336 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: This t-RNA occurs from Thermus thermophilus, in vitro transcription #2: Protein | Mass: 53988.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pK7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27000, glutamate-tRNA ligase #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 50.81 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: PEG1500, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 or 20 ℃ / pH: 6.5 / 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: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 12, 2001 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 426837 / Num. obs: 92817 / % possible obs: 96.4 % / Observed criterion σ(I): -0.3 / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.074 |
Reflection shell | Resolution: 2.1→2.2 Å / Rmerge(I) obs: 0.342 / % possible all: 88.5 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 426837 |
Reflection shell | *PLUS % possible obs: 88.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 1G59 Resolution: 2.1→49.36 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 5656722.2 / 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: 52.6101 Å2 / ksol: 0.342137 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→49.36 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.2 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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