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- PDB-6ve9: Solution NMR structure of enterococcal cytolysin S (CylLS") produ... -

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Basic information

Entry
Database: PDB / ID: 6ve9
TitleSolution NMR structure of enterococcal cytolysin S (CylLS") produced by Enterococcus faecalis
Componentsenterococcal cytolysin S
KeywordsTOXIN / lanthipeptide / cytolysin / cyclic peptide / posttranslational modification
Function / homologyType 2 lantibiotic, SP_1948 family / Two-component Enterococcus faecalis cytolysin (EFC) / defense response to Gram-positive bacterium / CylL-S protein
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsBobeica, S.C. / van der Donk, W.A. / Zhu, L. / Tang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37GM058822 United States
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
DepositionDec 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag ..._struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: enterococcal cytolysin S


Theoretical massNumber of molelcules
Total (without water)2,0371
Polymers2,0371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide enterococcal cytolysin S / CylLS"


Mass: 2037.470 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / References: UniProt: H7C7B5*PLUS
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
212isotropic12D 1H-1H TOCSY
222isotropic12D 1H-1H NOESY
131isotropic23D HN(CA)CB
141isotropic23D HN(CO)CA
151isotropic22D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM [U-99% 13C; U-99% 15N] Cytolysin S, methanolCylLS-15N-13Cmethanol
solution21.0 mM Cytolysin S, CD3OHCylLS-unlabeledCD3OH
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMCytolysin S[U-99% 13C; U-99% 15N]1
1.0 mMCytolysin Snatural abundance2
Sample conditions

Ionic strength: 0 Not defined / Ionic strength err: _ / pH: 6 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.001 / Temperature: 277 K / Temperature err: 0.1

Conditions-IDLabel
1CylLS-15N-13C-details
2CylLS-unlabeled-details

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Agilent VNMRSAgilentVNMRS7502

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Processing

NMR software
NameDeveloperClassification
SparkyGoddarddata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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