[English] 日本語
![](img/lk-miru.gif)
- PDB-1tyc: STRUCTURAL ANALYSIS OF A SERIES OF MUTANTS OF TYROSYL-TRNA SYNTHE... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1tyc | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURAL ANALYSIS OF A SERIES OF MUTANTS OF TYROSYL-TRNA SYNTHETASE: ENHANCEMENT OF CATALYSIS BY HYDROPHOBIC INTERACTIONS | ||||||
![]() | TYROSYL-tRNA SYNTHETASE | ||||||
![]() | AMINOACYL-TRNA SYNTHASE | ||||||
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 | ![]() | ||||||
![]() | Brown, K.A. / Brick, P. / De Meester, P. / Blow, D.M. | ||||||
![]() | ![]() Title: Structural Analysis of a Series of Mutants of Tyrosyl-tRNA Synthetase: Enhancement of Catalysis by Hydrophobic Interactions Authors: Brown, K.A. / De Meester, P. / Fersht II, A.R. / Blow, D.M. #1: ![]() Title: Structure of Tyrosyl-T/RNA Synthetase Refined at 2.3 Angstroms Resolution. Interaction of the Enzyme with the Tyrosyl Adenylate Intermediate Authors: Brick, P. / Bhat, T.N. / Blow, D.M. #2: ![]() Title: Crystal Structure of a Deletion Mutant of a Tyrosyl-T/RNA Synthetase Complexed with Tyrosine Authors: Brick, P. / Blow, D.M. #3: ![]() Title: Structure of a Mutant of Tyrosyl-tRNA Synthetase with Enhanced Catalytic Properties Authors: Brown, K.A. / Brick, P. / Blow, D.M. #4: ![]() Title: Internal Thermodynamics of Position 51 Mutants and Natural Variants of Tyrosyl-tRNA Synthetase Authors: Ho, C.K. / Fersht, A.R. #5: ![]() Title: Natural Variation of Tyrosyl-tRNA Synthetase and Comparison with Engineered Mutants Authors: Jones, M.D. / Lowe, D.M. / Borgford, T. / Fersht, A.R. #6: ![]() Title: Use of Binding Energy in Catalysis Analyzed by Mutagenesis of the Tyrosyl-tRNA Synthetase Authors: Wells, T.N.C. / Fersht, A.R. #7: ![]() Title: Fine Structure-Activity Analysis of Mutations at Position 51 of Tyrosyl-tRNA Synthetase Authors: Fersht, A.R. / Wilkinson, A.J. / Carter, P. / Winter, G. #8: ![]() Title: The Use of Double Mutants to Detect Structural Changes in the Active Site of the Tyrosyl-tRNA Synthetase (Bacillus Stearothermophilus) Authors: Carter, P.J. / Winter, G. / Wilkinson, A.J. / Fersht, A.R. #9: ![]() Title: A Large Increase in Enzyme-Substrate Affinity by Protein Engineering Authors: Wilkinson, A.J. / Fersht, A.R. / Blow, D.M. / Carter, P. / Winter, G. #10: ![]() 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. #11: ![]() Title: Tyrosyl-T/RNA Synthetase Forms a Mononucleotide-Binding Fold Authors: Bhat, T.N. / Blow, D.M. / Brick, P. / Nyborg, J. #12: ![]() Title: A Density-Modification Method for the Improvement of Poorly Resolved Protein Electron-Density Maps Authors: Bhat, T.N. / Blow, D.M. #13: ![]() Title: Binding of Tyrosine, Adenosine Triphosphate and Analogues to Crystalline Tyrosyl Transfer RNA Synthetase Authors: Monteilhet, C. / Blow, D.M. #14: ![]() Title: Structure of Aminoacyl T/RNA Synthetases Authors: Blow, D.M. / Monteilhet, C. / Rubin, J.R. #15: ![]() 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. #16: ![]() 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. #17: ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 78.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 58.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
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: ILE 158 - SIDE CHAIN BEYOND CB OMITTED. / 9: GLU 159 - SIDE CHAIN BEYOND CB OMITTED. / 10: THR 160 - SIDE CHAIN BEYOND CB OMITTED. / 11: ARG 214 - SIDE CHAIN BEYOND CB OMITTED. / 12: LYS 230 - SIDE CHAIN BEYOND CG OMITTED. / 13: LYS 233 - SIDE CHAIN BEYOND CB OMITTED. / 14: GLU 235 - SIDE CHAIN BEYOND CB OMITTED. / 15: SER 236 - SIDE CHAIN BEYOND CB OMITTED. / 16: GLU 276 - SIDE CHAIN BEYOND CG OMITTED. / 17: GLU 284 - SIDE CHAIN BEYOND CB OMITTED. / 18: GLU 287 - SIDE CHAIN BEYOND CG OMITTED. / 19: GLU 290 - SIDE CHAIN BEYOND CB OMITTED. / 20: LYS 291 - SIDE CHAIN BEYOND CG OMITTED. / 21: LYS 296 - SIDE CHAIN BEYOND CG OMITTED. / 22: GLU 310 - SIDE CHAIN BEYOND CB OMITTED. / 23: SER 319 - SIDE CHAIN BEYOND CB OMITTED. |
-
Components
#1: Protein | Mass: 36319.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P00952, tyrosine-tRNA ligase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.64 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
-
Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Highest resolution: 2.5 Å Details: THE 83 WATER MOLECULES WITH RESIDUE NUMBERS GREATER THAN 500 PROBABLY REPRESENT DISORDERED PROTEIN.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Num. reflection obs: 18160 / Rfactor obs: 0.219 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |