+
Open data
-
Basic information
Entry | Database: PDB / ID: 6y3g | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of phenylalanine tRNA from Escherichia coli | ||||||
![]() | RNA (75-MER) | ||||||
![]() | RNA / Transfer RNA with modifications | ||||||
Function / homology | GUANIDINE / RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bourgeois, G. / Mechulam, Y. / Schmitt, E. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates. Authors: Bourgeois, G. / Seguin, J. / Babin, M. / Gondry, M. / Mechulam, Y. / Schmitt, E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 117.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 77.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6y4bC ![]() 4ycoS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: RNA chain | Mass: 24620.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-GAI / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.95 Å3/Da / Density % sol: 75.14 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 12.4% PEG8000, 0.2M AcCa, 0.1M Hepes pH 7, 0.1M L-Pro |
-Data collection
Diffraction | Mean temperature: 278 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 9432 / % possible obs: 99.7 % / Redundancy: 12.5 % / CC1/2: 0.99 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 3.1→3.3 Å / Num. unique obs: 1464 / CC1/2: 0.68 / % possible all: 98.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4YCO Resolution: 3.1→42.98 Å / SU ML: 0.3628 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5042
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→42.98 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -18.976895582 Å / Origin y: -39.6366701535 Å / Origin z: -7.70185779636 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |