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Yorodumi- PDB-1n75: Crystal structure of Thermus thermophilus glutamyl-tRNA synthetas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n75 | ||||||
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Title | Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP. | ||||||
Components | Glutamyl-tRNA synthetase | ||||||
Keywords | LIGASE / ERS/ATP / Glutamyl-tRNA synthetase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
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: 1.9 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 | 1n75.cif.gz | 116.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n75.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 1n75.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/1n75 ftp://data.pdbj.org/pub/pdb/validation_reports/n7/1n75 | HTTPS FTP |
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-Related structure data
Related structure data | 1j09C 1n77C 1n78C 1glnS 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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1 |
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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.) 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 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ATP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 49.83 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG6000, 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: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jun 10, 2001 |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→50 Å / Num. all: 46014 / Num. obs: 46014 / % possible obs: 98.3 % / Observed criterion σ(I): -0.45 / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 1.89→1.98 Å / Rmerge(I) obs: 0.367 / % possible all: 96.9 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Num. measured all: 175753 |
Reflection shell | *PLUS % possible obs: 96.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 1GLN Resolution: 1.9→37.54 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2086690.04 / 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: 78.3668 Å2 / ksol: 0.399473 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→37.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 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: 1.9 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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