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- PDB-3ts1: STRUCTURE OF TYROSYL-T/RNA SYNTHETASE REFINED AT 2.3 ANGSTROMS RE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ts1 | ||||||
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Title | STRUCTURE OF TYROSYL-T/RNA SYNTHETASE REFINED AT 2.3 ANGSTROMS RESOLUTION. INTERACTION OF THE ENZYME WITH THE TYROSYL ADENYLATE INTERMEDIATE | ||||||
![]() | TYROSYL-TRNA SYNTHETASE | ||||||
![]() | LIGASE (SYNTHETASE) | ||||||
Function / homology | ![]() tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / regulation of protein complex stability / tRNA binding / protein homodimerization activity / protein-containing complex / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Monteilhet, C. / Brick, P. / Blow, D.M. | ||||||
![]() | ![]() Title: Structure of tyrosyl-tRNA synthetase refined at 2.3 A resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate. Authors: Brick, P. / Bhat, T.N. / Blow, D.M. #1: ![]() Title: Crystal Structure of a Deletion Mutant of a Tyrosyl-T/RNA Synthetase Complexed with Tyrosine Authors: Brick, P. / Blow, D.M. #2: ![]() Title: Interaction of Crystalline Tyrosol-T/RNA Synthetase with Adenosine, Adenosine Monophosphate, Adenosine Triphosphate and Pyrophosphate in the Presence of Tyrosinol Authors: Monteilhet, C. / Blow, D.M. / Brick, P. #3: ![]() Title: Tyrosyl-T/RNA Synthetase Forms a Mononucleotide-Binding Fold Authors: Bhat, T.N. / Blow, D.M. / Brick, P. / Nyborg, J. #4: ![]() Title: A Density-Modification Method for the Improvement of Poorly Resolved Protein Electron-Density Maps Authors: Bhat, T.N. / Blow, D.M. #5: ![]() Title: Binding of Tyrosine, Adenosine Triphosphate and Analogues to Crystalline Tyrosyl Transfer RNA Synthetase Authors: Monteilhet, C. / Blow, D.M. #6: ![]() Title: Structure of Aminoacyl T/RNA Synthetases Authors: Blow, D.M. / Monteilhet, C. / Rubin, J.R. #7: ![]() Title: The Peptide Chain of Tyrosyl T/RNA Synthetase. No Evidence for a Super-Secondary Structure of Four Alpha-Helices Authors: Blow, D.M. / Irwin, M.J. / Nyborg, J. #8: ![]() Title: The Crystal Structure of Tyrosyl-Transfer RNA Synthetase at 2.7 Angstroms Resolution Authors: Irwin, M.J. / Nyborg, J. / Reid, B.R. / Blow, D.M. #9: ![]() Title: Crystallization and Preliminary X-Ray Diffraction Studies on Tyrosyl-Transfer RNA Synthetase from Bacillus Stearothermophilus Authors: Reid, B.R. / Koch, G.L.E. / Boulanger, Y. / Hartley, B.S. / Blow, D.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.9 KB | Display | ![]() |
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PDB format | ![]() | 57.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 686.2 KB | Display | ![]() |
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Full document | ![]() | 702 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Atom site foot note | 1: MET 1 - SIDE CHAIN OMITTED. / 2: ASP 20 - SIDE CHAIN BEYOND CB OMITTED. / 3: ARG 30 - SIDE CHAIN BEYOND CB OMITTED. / 4: LYS 91 - SIDE CHAIN BEYOND CG OMITTED. / 5: GLU 92 - SIDE CHAIN BEYOND CB OMITTED. / 6: GLU 103 - SIDE CHAIN BEYOND CB OMITTED. / 7: GLU 112 - SIDE CHAIN BEYOND CB OMITTED. / 8: ASN 146 - SIDE CHAIN BEYOND CB OMITTED. / 9: ILE 158 - SIDE CHAIN BEYOND CB OMITTED. / 10: GLU 159 - SIDE CHAIN BEYOND CB OMITTED. / 11: THR 160 - SIDE CHAIN BEYOND CB OMITTED. / 12: ARG 214 - SIDE CHAIN BEYOND CB OMITTED. / 13: LYS 230 - SIDE CHAIN BEYOND CG OMITTED. / 14: LYS 233 - SIDE CHAIN BEYOND CB OMITTED. / 15: GLU 235 - SIDE CHAIN BEYOND CB OMITTED. / 16: SER 236 - SIDE CHAIN BEYOND CB OMITTED. / 17: GLU 276 - SIDE CHAIN BEYOND CG OMITTED. / 18: GLU 284 - SIDE CHAIN BEYOND CB OMITTED. / 19: GLU 287 - SIDE CHAIN BEYOND CG OMITTED. / 20: GLU 290 - SIDE CHAIN BEYOND CB OMITTED. / 21: LYS 291 - SIDE CHAIN BEYOND CG OMITTED. / 22: LYS 296 - SIDE CHAIN BEYOND CG OMITTED. / 23: GLU 310 - SIDE CHAIN BEYOND CB OMITTED. / 24: SER 319 - SIDE CHAIN BEYOND CB OMITTED. |
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Components
#1: Protein | Mass: 47364.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P00952, tyrosine-tRNA ligase |
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#2: Chemical | ChemComp-TYA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.54 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS |
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Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Highest resolution: 2.7 Å /
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Refinement step | Cycle: LAST / Highest resolution: 2.7 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.7 Å / Num. reflection obs: 12669 / Rfactor obs: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |