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Yorodumi- PDB-8ai6: Crystal structure of radical SAM epimerase EpeE D210A mutant from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ai6 | |||||||||
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Title | Crystal structure of radical SAM epimerase EpeE D210A mutant from Bacillus subtilis with [4Fe-4S] clusters, S-adenosyl-L-homocysteine and persulfurated cysteine bound | |||||||||
Components | Putative peptide biosynthesis protein YydG | |||||||||
Keywords | METAL BINDING PROTEIN / radical SAM / metalloenzyme / iron-sulfur / RiPP | |||||||||
Function / homology | Function and homology information catalytic activity / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Polsinelli, I. / Legrand, P. / Fyfe, C.D. / Benjdia, A. / Berteau, O. | |||||||||
Funding support | France, European Union, 2items
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Citation | Journal: Nat.Chem.Biol. / Year: 2024 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: Journal: Nat Chem / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ai6.cif.gz | 312.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ai6.ent.gz | 251.9 KB | Display | PDB format |
PDBx/mmJSON format | 8ai6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/8ai6 ftp://data.pdbj.org/pub/pdb/validation_reports/ai/8ai6 | HTTPS FTP |
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-Related structure data
Related structure data | 8ai1C 8ai2C 8ai3C 8ai4C 8ai5C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39940.500 Da / Num. of mol.: 2 / Mutation: D210A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: yydG, BSU40170 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q45595 |
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-Non-polymers , 5 types, 414 molecules
#2: Chemical | ChemComp-SF4 / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.78 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / Details: 15% (w/v) PEG 1000, 100 mM Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2021 |
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: 1.95→48.7 Å / Num. obs: 962748 / % possible obs: 100 % / Redundancy: 14.7 % / CC1/2: 0.975 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.036 / Rrim(I) all: 0.135 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.95→2 Å / Rmerge(I) obs: 2.032 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 74413 / CC1/2: 0.566 / Rpim(I) all: 0.532 / Rrim(I) all: 2.101 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Fe-SAD experimental model Resolution: 1.95→48.7 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.14 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.145 / SU Rfree Blow DPI: 0.126 / SU Rfree Cruickshank DPI: 0.124
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Displacement parameters | Biso mean: 51.69 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→48.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→1.96 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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