[English] 日本語
![](img/lk-miru.gif)
- PDB-8afj: tRNA modifying enzyme MiaE soaked in Na-dithionite in a glovebox ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8afj | ||||||
---|---|---|---|---|---|---|---|
Title | tRNA modifying enzyme MiaE soaked in Na-dithionite in a glovebox and flash-cooled using a miniature-airlock | ||||||
![]() | tRNA hydroxylase | ||||||
![]() | OXIDOREDUCTASE / anaerobic crystallisation / glove box / methodology | ||||||
Function / homology | ![]() tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine)-hydroxylase activity / tRNA modification / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | van der Linden, P. / Engilberge, S. / Atta, M. / Carpentier, P. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: tRNA modifying enzyme MiaE soaked in Na-dithionite in a glovebox and flash-cooled using a miniature-airlock Authors: van der Linden, P. / Engilberge, S. / Atta, M. / Carpentier, P. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 101.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 75.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 465.8 KB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 27.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zmbS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 22661.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 7 types, 263 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FE / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-1PE / | #6: Chemical | #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.77 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.5M CaCl2, 25% PEG 6 K and 0.2M Tris buffer at pH 8.5 and 10 mM sodium dithionite |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→47.41 Å / Num. obs: 37525 / % possible obs: 83.1 % / Redundancy: 3 % / CC1/2: 0.99 / Rrim(I) all: 0.062 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.59→1.79 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1808 / CC1/2: 0.71 / Rrim(I) all: 0.66 / % possible all: 55.1 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6ZMB Resolution: 1.6→40.62 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 31.06 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.02 Å2 / Biso mean: 28.36 Å2 / Biso min: 10.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→40.62 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
|