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- PDB-8ai3: Crystal structure of radical SAM epimerase EpeE C223A mutant from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ai3 | |||||||||
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Title | Crystal structure of radical SAM epimerase EpeE C223A mutant from Bacillus subtilis with [4Fe-4S] clusters and S-adenosyl-L-methionine 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. / Chavas, L.M.G. / Legrand, P. / Polsinelli, I. / 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 | ![]() | 301 KB | Display | ![]() |
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PDB format | ![]() | 242.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8ai1C ![]() 8ai2C ![]() 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: 39920.379 Da / Num. of mol.: 2 / Mutation: C223A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 327 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SF4 / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GOL / #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: 2.98 Å3/Da / Density % sol: 58.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12% (w/v) PEG 8000, 10% (v/v) Ethylene glycol, 0.1 M Hepes |
-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: Oct 5, 2017 / 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: 2.1→46.55 Å / Num. obs: 416209 / % possible obs: 99.7 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.03 / Rrim(I) all: 0.082 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.1→2.15 Å / Rmerge(I) obs: 1.891 / Mean I/σ(I) obs: 1 / Num. unique obs: 28724 / CC1/2: 0.509 / Rpim(I) all: 0.74 / Rrim(I) all: 2.035 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Fe-SAD Exprimental model Resolution: 2.1→40.27 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.958 / SU R Cruickshank DPI: 0.17 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.174 / SU Rfree Blow DPI: 0.14 / SU Rfree Cruickshank DPI: 0.139
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Displacement parameters | Biso mean: 64.84 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→40.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.11 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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