[English] 日本語
![](img/lk-miru.gif)
- PDB-6i8r: Crystal structure of an ancient sequence-reconstructed Elongation... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6i8r | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of an ancient sequence-reconstructed Elongation factor Tu (node 170) | |||||||||||||||
![]() | Elongation Factor Tu | |||||||||||||||
![]() | TRANSLATION / Protein Synthesis / Elongation Factor / Sequence reconstruction / ancient protein | |||||||||||||||
Function / homology | Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta / 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 170) Authors: Majumdar, S. / Bergfors, T. / Sanyal, S. | |||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 93.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 68 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 804.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 809.6 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dg1S S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 43870.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-GDP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.85 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 0.2 M Potassium Chloride, 20% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2→45.42 Å / Num. obs: 33564 / % possible obs: 99 % / Redundancy: 9.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.018 / Rrim(I) all: 0.055 / Net I/σ(I): 17.5 / Num. measured all: 325593 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1DG1 Resolution: 2→45.42 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / SU B: 8.351 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.153 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 263.76 Å2 / Biso mean: 66.933 Å2 / Biso min: 43 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→45.42 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.997→2.049 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|