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Yorodumi- PDB-1eqr: CRYSTAL STRUCTURE OF FREE ASPARTYL-TRNA SYNTHETASE FROM ESCHERICH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eqr | ||||||
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Title | CRYSTAL STRUCTURE OF FREE ASPARTYL-TRNA SYNTHETASE FROM ESCHERICHIA COLI | ||||||
Components | ASPARTYL-TRNA SYNTHETASE | ||||||
Keywords | LIGASE / Domains / anti-parallel beta strand / beta barrel / oligomer binding fold | ||||||
Function / homology | Function and homology information aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / nucleic acid binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Rees, B. / Webster, G. / Delarue, M. / Boeglin, M. / Moras, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Aspartyl tRNA-synthetase from Escherichia coli: flexibility and adaptability to the substrates. Authors: Rees, B. / Webster, G. / Delarue, M. / Boeglin, M. / Moras, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eqr.cif.gz | 355 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eqr.ent.gz | 289.8 KB | Display | PDB format |
PDBx/mmJSON format | 1eqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/1eqr ftp://data.pdbj.org/pub/pdb/validation_reports/eq/1eqr | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 65996.312 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PBLUESCRIPT-ASPS / Production host: Escherichia coli (E. coli) / References: UniProt: P21889, aspartate-tRNA ligase #2: Chemical | #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: 3 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: ammonium sulphate, Bis Tris propane, isopropanol, NaCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 288 KDetails: Boeglin, M., (1996) Acta Crystallog. sect., D52, 211. | ||||||||||||||||||||||||||||||||||||||||||||||||
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: LURE / Beamline: DW32 / Wavelength: 0.97 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 27, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→30 Å / Num. all: 60472 / Num. obs: 67041 / % possible obs: 90.2 % / Observed criterion σ(F): -10 / Redundancy: 1.76 % / Biso Wilson estimate: 49.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 2.7 / Num. unique all: 8888 / % possible all: 92.3 |
Reflection | *PLUS Num. all: 67041 / Num. obs: 60472 |
Reflection shell | *PLUS % possible obs: 92.3 % / Num. unique obs: 8888 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: E.coli aspartyl-tRNA synthetase - S. cerevisiae tRNA(Asp) complex (Moulinier, unpublished) Resolution: 2.7→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2733513.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.4303 Å2 / ksol: 0.343238 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 4.9 % / Rfactor obs: 0.197 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 38.3 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.393 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.29 |