[English] 日本語
![](img/lk-miru.gif)
- PDB-1qu3: INSIGHTS INTO EDITING FROM AN ILE-TRNA SYNTHETASE STRUCTURE WITH ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1qu3 | ||||||
---|---|---|---|---|---|---|---|
Title | INSIGHTS INTO EDITING FROM AN ILE-TRNA SYNTHETASE STRUCTURE WITH TRNA(ILE) AND MUPIROCIN | ||||||
![]() |
| ||||||
![]() | LIGASE/RNA / SHUTTLING MECHANISM / EDITING TRNA SYNTHETASE / DOUBLE-SIEVE / METAL IONS / HYDROLYTIC FUNCTION / LIGASE-RNA COMPLEX | ||||||
Function / homology | ![]() isoleucine-tRNA ligase / isoleucine-tRNA ligase activity / isoleucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / tRNA binding / zinc ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Silvian, L.F. / Wang, J. / Steitz, T.A. | ||||||
![]() | ![]() Title: Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin. Authors: Silvian, L.F. / Wang, J. / Steitz, T.A. #1: ![]() Title: Metal Ions that Stabilize the tRNA and Mediate the Recognition by its Cognate Synthetase Authors: Wang, J. / Silvian, L.F. / Steitz, T.A. #2: ![]() Title: Switching from a Resting to Synthetic and Hydrolytic Modes in Editing tRNA Synthetases Authors: Wang, J. / Silvian, L.F. / Steitz, T.A. #3: ![]() Title: Structure Based Drug Design Against Mupirocin Resistant Staphylococcus Aureus Authors: Wang, J. / Silvian, L.F. / Steitz, T.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 237.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 181.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 668.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 783.4 KB | Display | |
Data in XML | ![]() | 51.3 KB | Display | |
Data in CIF | ![]() | 71.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-
Components
#1: RNA chain | Mass: 24236.381 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 105057.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-MRC / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.21 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: evaporation / Details: EVAPORATION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PRINCETON 2K / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→100 Å / Num. all: 23256 / Num. obs: 23256 / % possible obs: 89.5 % / Biso Wilson estimate: 38.5 Å2 / Rsym value: 0.099 |
Reflection | *PLUS Rmerge(I) obs: 0.099 |
-
Processing
Refinement | Resolution: 2.9→10 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 375201.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.25 Å2 / ksol: 0.312 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 4.7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.394 / % reflection Rfree: 5.7 % / Rfactor Rwork: 0.36 |