+
Open data
-
Basic information
Entry | Database: PDB / ID: 5gra | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of TrmJ from Z. mobilis ZM4 | ||||||
![]() | tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ | ||||||
![]() | ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gu, D.-H. / Kim, J.-S. | ||||||
![]() | ![]() Title: An asymmetric dimeric structure of TrmJ tRNA methyltransferase from Zymomonas mobilis with a flexible C-terminal dimer Authors: Gu, D.-H. / Park, M.-Y. / Kim, J.-S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 186.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 150.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 26466.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 31821 / ZM4 / CP4 / Gene: trmJ, ZMO1203 / Production host: ![]() ![]() ![]() References: UniProt: Q5NN83, ![]() #2: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.76 % |
---|---|
Crystal grow![]() | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: Ammonium Sulfate, MES, Lithium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3→50 Å / Num. obs: 19496 / % possible obs: 97.7 % / Redundancy: 1.8 % / Net I/σ(I): 4.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 3.005→40.656 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.58
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.005→40.656 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 43.5687 Å / Origin y: -22.5466 Å / Origin z: 52.58 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |