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Yorodumi- PDB-6vgt: Solution NMR structure of enterococcal cytolysin L (CylLL") produ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vgt | |||||||||
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Title | Solution NMR structure of enterococcal cytolysin L (CylLL") produced by Enterococcus faecalis | |||||||||
Components | cytolysin L | |||||||||
Keywords | TOXIN / lanthipeptide / cytolysin / cyclic peptide / posttranslational modification | |||||||||
Function / homology | Two-component Enterococcus faecalis cytolysin (EFC) / Type 2 lantibiotic, SP_1948 family / defense response to Gram-positive bacterium / CylL-L protein Function and homology information | |||||||||
Biological species | Enterococcus faecalis (bacteria) | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
Authors | Bobeica, S.C. / van der Donk, W.A. / Zhu, L. / Tang, W. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Chem Sci / Year: 2020 Title: Structural determinants of macrocyclization in substrate-controlled lanthipeptide biosynthetic pathways. Authors: Bobeica, S.C. / Zhu, L. / Acedo, J.Z. / Tang, W. / van der Donk, W.A. #1: Journal: Chem Sci / Year: 2020 Title: Correction: Structural determinants of macrocyclization in substrate-controlled lanthipeptide biosynthetic pathways. Authors: Bobeica, S.C. / Zhu, L. / Acedo, J.Z. / Tang, W. / van der Donk, W.A. #2: Journal: Nat.Chem.Biol. / Year: 2013 Title: The sequence of the enterococcal cytolysin imparts unusual lanthionine stereochemistry. Authors: Tang, W. / van der Donk, W.A. #3: Journal: Nat.Chem.Biol. / Year: 2013 Title: The sequence of the enterococcal cytolysin imparts unusual lanthionine stereochemistry. Authors: Tang, W. / van der Donk, W.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vgt.cif.gz | 190.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vgt.ent.gz | 160.3 KB | Display | PDB format |
PDBx/mmJSON format | 6vgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vgt_validation.pdf.gz | 448 KB | Display | wwPDB validaton report |
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Full document | 6vgt_full_validation.pdf.gz | 626.6 KB | Display | |
Data in XML | 6vgt_validation.xml.gz | 39.6 KB | Display | |
Data in CIF | 6vgt_validation.cif.gz | 46.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/6vgt ftp://data.pdbj.org/pub/pdb/validation_reports/vg/6vgt | HTTPS FTP |
-Related structure data
Related structure data | 6ve9C 6vhjC 6vjqC 6vljC 7ju9C 7jvfC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3446.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: H7C7B0*PLUS |
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Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution / Contents: 2.0 mM cytolysin L, methanol / Details: CD3-OH with DSS standard / Label: CylLL" / Solvent system: methanol |
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Sample | Conc.: 2.0 mM / Component: cytolysin L / Isotopic labeling: natural abundance |
Sample conditions | Ionic strength: 0 Not defined / Ionic strength err: 0 / Label: CylLL"_details / pH: 6 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0 / Temperature: 296 K / Temperature err: 0.1 |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 6 | ||||||||||||||||||||||||
NMR representative | Selection criteria: medoid | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |