[English] 日本語
![](img/lk-miru.gif)
- PDB-6q56: Crystal structure of the B. subtilis M1A22 tRNA methyltransferase TrmK -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6q56 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the B. subtilis M1A22 tRNA methyltransferase TrmK | ||||||
![]() | tRNA (adenine(22)-N(1))-methyltransferase | ||||||
![]() | RNA BINDING PROTEIN / methyltransferase / tRNA methyltransferase | ||||||
Function / homology | ![]() tRNA (adenine22-N1)-methyltransferase / : / tRNA methylation / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Degut, C. / Roovers, M. / Barraud, P. / Brachet, F. / Feller, A. / Larue, V. / Al Refaii, A. / Caillet, J. / Droogmans, L. / Tisne, C. | ||||||
![]() | ![]() Title: Structural characterization of B. subtilis m1A22 tRNA methyltransferase TrmK: insights into tRNA recognition. Authors: Degut, C. / Roovers, M. / Barraud, P. / Brachet, F. / Feller, A. / Larue, V. / Al Refaii, A. / Caillet, J. / Droogmans, L. / Tisne, C. #1: ![]() Title: Backbone resonance assignments of the m1A22 tRNA methyltransferase TrmK from Bacillus subtilis. Authors: Degut, C. / Barraud, P. / Larue, V. / Tisne, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 193.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 155.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 472.5 KB | Display | |
Data in XML | ![]() | 38 KB | Display | |
Data in CIF | ![]() | 53.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ku1S S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 26165.803 Da / Num. of mol.: 4 / Mutation: C35S C152S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: trmK, yqfN, BSU25180 / Production host: ![]() ![]() References: UniProt: P54471, tRNA (adenine22-N1)-methyltransferase #2: Chemical | ChemComp-NI / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.2 M ammonium acetate 0.1 M sodium acetate trihydrate pH 5 30% w/v polyethylene glycol 4000 8% 2-Methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→46.24 Å / Num. obs: 57747 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 32.71 Å2 / Rmerge(I) obs: 0.2108 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.98→2.175 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.451 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 4968 / CC1/2: 0.227 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3KU1 Resolution: 2→46.239 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.87 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→46.239 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|