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- PDB-8ai1: Crystal structure of radical SAM epimerase EpeE from Bacillus sub... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ai1 | |||||||||
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Title | Crystal structure of radical SAM epimerase EpeE from Bacillus subtilis with [4Fe-4S] clusters and S-adenosyl-L-homocysteine bound. | |||||||||
![]() | Putative peptide biosynthesis protein YydG | |||||||||
![]() | 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 | ![]() ![]() ![]() | |||||||||
![]() | Kubiak, X. / Polsinelli, I. / Chavas, L.M.G. / Legrand, P. / Fyfe, C.D. / Benjdia, A. / Berteau, O. | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 292.3 KB | Display | ![]() |
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PDB format | ![]() | 236.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 26.2 KB | Display | |
Data in CIF | ![]() | 37.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ai2C ![]() 8ai3C ![]() 8ai4C ![]() 8ai5C ![]() 8ai6C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39952.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 204 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)
#2: Chemical | ChemComp-SF4 / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PEG / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 17.5% (w/v) PEG 1000, 0.1 M Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: 2.4→48.97 Å / Num. obs: 534028 / % possible obs: 99.8 % / Redundancy: 14.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.038 / Rrim(I) all: 0.146 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 1.595 / Num. unique obs: 48252 / CC1/2: 0.724 / Rpim(I) all: 0.46 / Rrim(I) all: 1.661 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Fe-SAD Exprimental model Resolution: 2.4→48.96 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.295 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.302 / SU Rfree Blow DPI: 0.208 / SU Rfree Cruickshank DPI: 0.209
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Displacement parameters | Biso mean: 66.65 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→48.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.42 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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