[English] 日本語
![](img/lk-miru.gif)
- PDB-8h98: Crystal structure of chemically modified E. coli ThrS catalytic d... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8h98 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of chemically modified E. coli ThrS catalytic domain 1 | ||||||
![]() | Threonine--tRNA ligase | ||||||
![]() | LIGASE / Threonine--tRNA ligase | ||||||
Function / homology | ![]() 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 / cytoplasm / 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 | ![]() | 349.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 282.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1022.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 33.3 KB | Display | |
Data in CIF | ![]() | 47.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h99C ![]() 8h9aC ![]() 8h9bC ![]() 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: 47927.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.18 % |
---|---|
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 9, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 36908 / % possible obs: 97 % / Redundancy: 4.4 % / Biso Wilson estimate: 41.78 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 1.03 / Num. unique obs: 1021 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1FYF Resolution: 2.5→49.28 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 29.59 / 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: 118.12 Å2 / Biso mean: 48.1872 Å2 / Biso min: 25.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→49.28 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 14.2689 Å / Origin y: 26.5611 Å / Origin z: 37.1201 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|