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- PDB-6vgt: Solution NMR structure of enterococcal cytolysin L (CylLL") produ... -

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Basic information

Entry
Database: PDB / ID: 6vgt
TitleSolution NMR structure of enterococcal cytolysin L (CylLL") produced by Enterococcus faecalis
Componentscytolysin L
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-L 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
DepositionJan 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 2.0Sep 9, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / entity_name_com ...atom_site / entity_name_com / pdbx_entity_instance_feature / pdbx_nmr_refine / pdbx_nmr_representative / pdbx_struct_assembly / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_representative.selection_criteria / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _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
Description: Chirality error
Details: Residue ABA 1 should have been (R) configuration at CB. An additional improper angle was defined in the XPLOR patch command to ensure (R) configuration at CB of ABA in LL (methyl) ...Details: Residue ABA 1 should have been (R) configuration at CB. An additional improper angle was defined in the XPLOR patch command to ensure (R) configuration at CB of ABA in LL (methyl) lanthionine linkages is maintained.
Provider: author / Type: Coordinate replacement
Revision 2.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Revision 2.2Jun 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: cytolysin L


Theoretical massNumber of molelcules
Total (without water)3,4461
Polymers3,4461
Non-polymers00
Water00
1


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

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Components

#1: Protein/peptide cytolysin L


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
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
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 2.0 mM cytolysin L, methanol / Details: CD3-OH with DSS standard / Label: CylLL" / Solvent system: methanol
SampleConc.: 2.0 mM / Component: cytolysin L / Isotopic labeling: natural abundance
Sample conditionsIonic 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

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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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
SparkyGoddardpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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