[English] 日本語
![](img/lk-miru.gif)
- PDB-4yvh: Crystal Structure of H. influenzae TrmD in complex with sinefungin -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4yvh | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of H. influenzae TrmD in complex with sinefungin | ||||||
![]() | tRNA (guanine-N(1)-)-methyltransferase![]() | ||||||
![]() | ![]() | ||||||
Function / homology | ![]() tRNA N1-guanine methylation / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yoshida, K. / Ito, T. / Yokoyama, S. | ||||||
![]() | ![]() Title: Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD. Authors: Ito, T. / Masuda, I. / Yoshida, K. / Goto-Ito, S. / Sekine, S. / Suh, S.W. / Hou, Y.M. / Yokoyama, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 70.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 49.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4yvgC ![]() 4yviC ![]() 4yvjC ![]() 4yvkC ![]() 1uajS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | ![]() Mass: 29750.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: trmD, HI_0202 / Production host: ![]() ![]() ![]() References: UniProt: P43912, ![]() |
---|---|
#2: Chemical | ChemComp-SFG / |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.38 % |
---|---|
Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: sodium citrate, CHES |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.6→50 Å / Num. obs: 39872 / % possible obs: 99.8 % / Redundancy: 6.1 % / Net I/σ(I): 30.2 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 1UAJ Resolution: 1.6→23.241 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.41 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.62 Å2 / ksol: 0.397 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→23.241 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|