[English] 日本語
![](img/lk-miru.gif)
- PDB-7bbn: Crystal structure of an ancient sequence-reconstructed Elongation... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7bbn | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of an ancient sequence-reconstructed Elongation Factor Tu (node 317) | |||||||||||||||
![]() | Elongation Factor Tu | |||||||||||||||
![]() | TRANSLATION / Protein synthesis / Elongation Factor / ancestral sequence reconstruction / evolution | |||||||||||||||
Function / homology | GUANOSINE-5'-DIPHOSPHATE![]() | |||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Majumdar, S. / Bergfors, T. / Sanyal, S. | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() Title: Crystal structure of an ancient sequence-reconstructed Elongation factor Tu (node 317) Authors: Majumdar, S. / Bergfors, T. / Sanyal, S. | |||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 161.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 125.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 30.9 KB | Display | |
Data in CIF | ![]() | 44.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1efcS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 43124.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 0.2 M Lithium citrate tribasic tetrathydrate, 20% w/v PEG 3350, pH 8.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.918401 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.68→29.44 Å / Num. obs: 88432 / % possible obs: 98.9 % / Redundancy: 11 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.029 / Rrim(I) all: 0.098 / Net I/σ(I): 14.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1EFC Resolution: 1.68→29.44 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.048 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.101 / 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: 83.57 Å2 / Biso mean: 24.52 Å2 / Biso min: 10.22 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.68→29.44 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.681→1.724 Å / Rfactor Rfree error: 0
|