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Yorodumi- PDB-8ai4: Crystal structure of radical SAM epimerase EpeE C223A mutant from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ai4 | |||||||||
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Title | Crystal structure of radical SAM epimerase EpeE C223A mutant from Bacillus subtilis with [4Fe-4S] clusters, S-adenosyl-L-homocysteine and RiPP peptide 5 bound | |||||||||
Components |
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Keywords | METAL BINDING PROTEIN / radical SAM / metalloenzyme / iron-sulfur / RiPP | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Polsinelli, I. / Fyfe, C.D. / Legrand, P. / Kubiak, X. / Chavas, L.M.G. / Berteau, O. / Benjdia, A. | |||||||||
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 | 8ai4.cif.gz | 318.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ai4.ent.gz | 256.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ai4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ai4_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 8ai4_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 8ai4_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 8ai4_validation.cif.gz | 48.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/8ai4 ftp://data.pdbj.org/pub/pdb/validation_reports/ai/8ai4 | HTTPS FTP |
-Related structure data
Related structure data | 8ai1C 8ai2C 8ai3C 8ai5C 8ai6C 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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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 39920.379 Da / Num. of mol.: 2 / Mutation: C223A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_2355 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0A1MJP5 #2: Protein/peptide | Mass: 1422.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria) / References: UniProt: Q45596 |
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-Non-polymers , 6 types, 582 molecules
#3: Chemical | ChemComp-SF4 / #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PEG / #7: Chemical | ChemComp-GOL / | #8: 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: 2.8 Å3/Da / Density % sol: 56.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG 1000, Tris 0.1 M. |
-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: Sep 10, 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: 1.75→46.04 Å / Num. obs: 1406836 / % possible obs: 100 % / Redundancy: 15 % / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.018 / Rrim(I) all: 0.069 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.75→1.8 Å / Rmerge(I) obs: 2.073 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 91475 / CC1/2: 0.518 / Rpim(I) all: 0.589 / Rrim(I) all: 2.157 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Fe-SAD experimental model Resolution: 1.75→43.56 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.095 / SU Rfree Blow DPI: 0.089 / SU Rfree Cruickshank DPI: 0.086
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Displacement parameters | Biso mean: 43.64 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→43.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.76 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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