[English] 日本語
![](img/lk-miru.gif)
- PDB-8ai2: Crystal structure of radical SAM epimerase EpeE from Bacillus sub... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8ai2 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of radical SAM epimerase EpeE from Bacillus subtilis with [4Fe-4S] clusters, S-adenosyl-L-homocysteine and RiPP peptide 5 bound | |||||||||
![]() |
| |||||||||
![]() | METAL BINDING PROTEIN / radical SAM / metalloenzyme / iron-sulfur / RiPP | |||||||||
Function / homology | ![]() catalytic activity / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Polsinelli, I. / Fyfe, C.D. / Legrand, P. / Kubiak, X. / Chavas, L.M.G. / Berteau, O. / Benjdia, A. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural and mechanistic basis for RiPP epimerization by a radical SAM enzyme. Authors: Kubiak, X. / Polsinelli, I. / Chavas, L.M.G. / Fyfe, C.D. / Guillot, A. / Fradale, L. / Brewee, C. / Grimaldi, S. / Gerbaud, G. / Thureau, A. / Legrand, P. / Berteau, O. / Benjdia, A. #1: ![]() Title: Post-translational modification of ribosomally synthesized peptides by a radical SAM epimerase in Bacillus subtilis. Authors: Benjdia, A. / Guillot, A. / Ruffie, P. / Leprince, J. / Berteau, O. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 302.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 244.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 28.1 KB | Display | |
Data in CIF | ![]() | 39.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ai1C ![]() 8ai3C ![]() 8ai4C ![]() 8ai5C ![]() 8ai6C C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-
Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 39952.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 1422.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
---|
-Non-polymers , 5 types, 243 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SF4 / #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PEG / #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.37 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 14% (w/v) PEG 1000, Tris 0.1 M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 15, 2021 / Details: KB Mirrors |
Radiation | Monochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→46.19 Å / Num. obs: 571609 / % possible obs: 99.9 % / Redundancy: 15.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.031 / Rrim(I) all: 0.122 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.39→2.48 Å / Rmerge(I) obs: 1.411 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 60066 / CC1/2: 0.84 / Rpim(I) all: 0.366 / Rrim(I) all: 1.458 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: Fe-SAD Exprimental model Resolution: 2.393→46.19 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.285 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.293 / SU Rfree Blow DPI: 0.209 / SU Rfree Cruickshank DPI: 0.209
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.94 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.28 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.393→46.19 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.393→2.41 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|