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Yorodumi- PDB-1tky: Crystal structure of the editing domain of threonyl-tRNA syntheta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tky | ||||||
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Title | Crystal structure of the editing domain of threonyl-tRNA synthetase complexed with seryl-3'-aminoadenosine | ||||||
Components | Threonyl-tRNA synthetase | ||||||
Keywords | LIGASE | ||||||
Function / homology | Function and homology information tRNA aminoacylation / aminoacyl-tRNA ligase activity / threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding ...tRNA aminoacylation / aminoacyl-tRNA ligase activity / threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding / regulation of translation / tRNA binding / response to antibiotic / protein homodimerization activity / RNA binding / zinc ion binding / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Dock-Bregeon, A.C. / Rees, B. / Torres-Larios, A. / Bey, G. / Caillet, J. / Moras, D. | ||||||
Citation | Journal: Mol.Cell / Year: 2004 Title: Achieving Error-Free Translation; The Mechanism of Proofreading of Threonyl-tRNA Synthetase at Atomic Resolution. Authors: Dock-Bregeon, A.C. / Rees, B. / Torres-Larios, A. / Bey, G. / Caillet, 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 | 1tky.cif.gz | 65.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tky.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 1tky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tky_validation.pdf.gz | 715.9 KB | Display | wwPDB validaton report |
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Full document | 1tky_full_validation.pdf.gz | 718.3 KB | Display | |
Data in XML | 1tky_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 1tky_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/1tky ftp://data.pdbj.org/pub/pdb/validation_reports/tk/1tky | HTTPS FTP |
-Related structure data
Related structure data | 1tjeC 1tkeC 1tkgC 1qf6S S: Starting model for refinement C: citing same article (ref.) |
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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: 25465.930 Da / Num. of mol.: 1 / Fragment: Domains N1 and N2 (residues 1-224) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: THRS, B1719, C2116, SF1512, S1630 / Plasmid: peT28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A8M3, threonine-tRNA ligase |
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#2: Chemical | ChemComp-A3S / |
#3: 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: 2.24 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, Tris.cl, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.933 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 24, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→29.52 Å / Num. all: 39904 / Num. obs: 39904 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.071 |
Reflection shell | Resolution: 1.47→1.52 Å / Rmerge(I) obs: 0.228 / Num. unique all: 3696 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1QF6 Resolution: 1.48→29.52 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1236769.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.908 Å2 / ksol: 0.39751 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.48→29.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.48→1.53 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
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Xplor file |
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