[English] 日本語
![](img/lk-miru.gif)
- PDB-8h9b: Crystal structure of chemically modified E. coli ThrS catalytic d... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8h9b | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of chemically modified E. coli ThrS catalytic domain 3 | ||||||
![]() | Threonine--tRNA ligase | ||||||
![]() | LIGASE / Threonine--tRNA ligase | ||||||
Function / homology | ![]() threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA binding / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Qiao, H. / Xia, M. / Wang, J. / Fang, P. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Tyrosine-targeted covalent inhibition of a tRNA synthetase aided by zinc ion. Authors: Qiao, H. / Xia, M. / Cheng, Y. / Zhou, J. / Zheng, L. / Li, W. / Wang, J. / Fang, P. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 180.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 140 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 743.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 746.6 KB | Display | |
Data in XML | ![]() | 17.3 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h98C ![]() 8h99C ![]() 8h9aC ![]() 8h9cC ![]() 1fyfS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 47893.523 Da / Num. of mol.: 1 / Fragment: UNP residues 242-642 / Mutation: Y462K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-X5V / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.71 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.03 M diethylene glycol, 0.03 M triethylene glycol, 0.03 M tetraehylene glycol, 0.03 M pentaethylene glycol, 0.05 M sodium HEPES, 0.05 M MOPS (acid), pH 7.5, 20% v/v ethylene glycol, 10% w/v PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 11640 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.2→2.27 Å / Rmerge(I) obs: 1.072 / Num. unique obs: 2647 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1FYF Resolution: 2.23→40.36 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.54 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.93 Å2 / Biso mean: 38.721 Å2 / Biso min: 24.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.23→40.36 Å
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
| ||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -19.8757 Å / Origin y: -37.0141 Å / Origin z: -12.0851 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|