[English] 日本語
![](img/lk-miru.gif)
- PDB-7wq0: Methionyl-tRNA synthetase from Staphylococcus aureus complexed wi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7wq0 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Methionyl-tRNA synthetase from Staphylococcus aureus complexed with a fragment and ATP | |||||||||
![]() | Methionine--tRNA ligase | |||||||||
![]() | LIGASE/INHIBITOR / LIGASE-INHIBITOR COMPLEX | |||||||||
Function / homology | ![]() methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yi, J. / Cai, Z. / Qiu, H. / Lu, F. / Chen, B. / Luo, Z. / Gu, Q. / Xu, J. / Zhou, H. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Fragment screening and structural analyses highlight the ATP-assisted ligand binding for inhibitor discovery against type 1 methionyl-tRNA synthetase. Authors: Yi, J. / Cai, Z. / Qiu, H. / Lu, F. / Luo, Z. / Chen, B. / Gu, Q. / Xu, J. / Zhou, H. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 121.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 89.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wpiC ![]() 7wpjC ![]() 7wpkSC ![]() 7wplC ![]() 7wpmC ![]() 7wpnC ![]() 7wptC ![]() 7wpxC 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: 61103.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: COL / Gene: metG / Production host: ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-ATP / | ||||
#3: Chemical | ChemComp-TPA / | ||||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.25 % |
---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Sodium cacodylate, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97914 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→46.02 Å / Num. obs: 30973 / % possible obs: 99.7 % / Redundancy: 6.5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.065 / Rrim(I) all: 0.167 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.09→2.15 Å / Redundancy: 6 % / Rmerge(I) obs: 0.508 / Num. unique obs: 2306 / CC1/2: 0.872 / Rpim(I) all: 0.225 / Rrim(I) all: 0.557 / % possible all: 97 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 7WPK Resolution: 2.09→46.02 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.891 / SU B: 5.5 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.66 Å2 / Biso mean: 19.778 Å2 / Biso min: 5.76 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.09→46.02 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.092→2.146 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|