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Yorodumi- PDB-1efw: Crystal structure of aspartyl-tRNA synthetase from Thermus thermo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1efw | ||||||
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Title | Crystal structure of aspartyl-tRNA synthetase from Thermus thermophilus complexed to tRNAasp from Escherichia coli | ||||||
Components |
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Keywords | LIGASE/RNA / ASPARTYL-TRNA SYNTHETASE / TRNA / PROTEIN-RNA COMPLEX / LIGASE-RNA complex | ||||||
Function / homology | Function and homology information aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / nucleic acid binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å | ||||||
Authors | Briand, C. / Poterszman, A. / Eiler, S. / Webster, G. / Thierry, J.-C. / Moras, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: An intermediate step in the recognition of tRNA(Asp) by aspartyl-tRNA synthetase. Authors: Briand, C. / Poterszman, A. / Eiler, S. / Webster, G. / Thierry, J. / Moras, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1efw.cif.gz | 325.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1efw.ent.gz | 258.4 KB | Display | PDB format |
PDBx/mmJSON format | 1efw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1efw_validation.pdf.gz | 501.8 KB | Display | wwPDB validaton report |
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Full document | 1efw_full_validation.pdf.gz | 620 KB | Display | |
Data in XML | 1efw_validation.xml.gz | 63.7 KB | Display | |
Data in CIF | 1efw_validation.cif.gz | 87.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/1efw ftp://data.pdbj.org/pub/pdb/validation_reports/ef/1efw | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 23724.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) #2: Protein | Mass: 66124.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P36419, aspartate-tRNA ligase #3: 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: 4.5 Å3/Da / Density % sol: 72.68 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: sodium citrate, magnesium chloride, Na-HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 17 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3→15 Å / Num. all: 58634 / Num. obs: 58634 / % possible obs: 91.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 51.1 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.239 / Num. unique all: 6249 / % possible all: 98.3 |
Reflection shell | *PLUS % possible obs: 98.3 % / Mean I/σ(I) obs: 5.4 |
-Processing
Software |
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Refinement | Resolution: 3→15 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3265212.52 / 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: 17.73 Å2 / ksol: 0.322 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: 'CNS' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 55665 / % reflection Rfree: 4.7 % / Rfactor obs: 0.246 / Rfactor Rfree: 0.291 / Rfactor Rwork: 0.246 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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