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- PDB-6t33: The unusual structure of Ruminococcin C1 antimicrobial peptide co... -

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Basic information

Entry
Database: PDB / ID: 6t33
TitleThe unusual structure of Ruminococcin C1 antimicrobial peptide confers activity against clinical pathogens
ComponentsRuminococcin C
KeywordsANTIMICROBIAL PROTEIN / bacteriocin / ruminoccin / antibiotic / thioether bridge
Function / homologyRuminococcin C
Function and homology information
Biological species[Ruminococcus] gnavus E1 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsChiumento, S. / Roblin, C. / Bornet, O. / Nouailler, M. / Muller, C. / Basset, C. / Kieffer-Jaquinod, S. / Coute, Y. / Torelli, S. / Le Pape, L. ...Chiumento, S. / Roblin, C. / Bornet, O. / Nouailler, M. / Muller, C. / Basset, C. / Kieffer-Jaquinod, S. / Coute, Y. / Torelli, S. / Le Pape, L. / Shunemann, V. / Jeannot, K. / Nicoletti, C. / Iranzo, O. / Maresca, M. / Giardina, T. / Fons, M. / Devillard, E. / Perrier, J. / Atta, M. / Guerlesquin, F. / Lafond, M. / Duarte, V.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE21-0020 France
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: The unusual structure of Ruminococcin C1 antimicrobial peptide confers clinical properties.
Authors: Roblin, C. / Chiumento, S. / Bornet, O. / Nouailler, M. / Muller, C.S. / Jeannot, K. / Basset, C. / Kieffer-Jaquinod, S. / Coute, Y. / Torelli, S. / Le Pape, L. / Schunemann, V. / Olleik, H. ...Authors: Roblin, C. / Chiumento, S. / Bornet, O. / Nouailler, M. / Muller, C.S. / Jeannot, K. / Basset, C. / Kieffer-Jaquinod, S. / Coute, Y. / Torelli, S. / Le Pape, L. / Schunemann, V. / Olleik, H. / De La Villeon, B. / Sockeel, P. / Di Pasquale, E. / Nicoletti, C. / Vidal, N. / Poljak, L. / Iranzo, O. / Giardina, T. / Fons, M. / Devillard, E. / Polard, P. / Maresca, M. / Perrier, J. / Atta, M. / Guerlesquin, F. / Lafond, M. / Duarte, V.
History
DepositionOct 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
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
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ruminococcin C


Theoretical massNumber of molelcules
Total (without water)4,3341
Polymers4,3341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3120 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Ruminococcin C


Mass: 4333.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Four cysteine sulfur to alpha-carbon cross-links between C3/N16, C5/A12, C22/K42 and C26/R34 D stereochemistry at Ala12 (alpha-S), Asn16 (alpha-S), Arg34 (alpha-S) and Lys42 (alpha-S)
Source: (gene. exp.) [Ruminococcus] gnavus E1 (bacteria) / Gene: rumC1 / Production host: Escherichia coli (E. coli) / References: UniProt: F8QV07
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
212isotropic22D 1H-15N HSQC
222isotropic22D 1H-13C HSQC
262isotropic23D 1H-15N NOESY
2152isotropic23D 1H-15N TOCSY
272isotropic23D HNHA
232isotropic23D HNCA
242isotropic23D HN(CO)CA
252isotropic23D HN(CA)CB
2112isotropic23D CBCA(CO)NH
2102isotropic23D HNCO
292isotropic23D HN(CA)CO
282isotropic23D (H)CCH-TOCSY
1142isotropic12D 1H-1H TOCSY
1132isotropic12D 1H-1H NOESY
1122isotropic12D DQF-COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12 mM Ruminococcin C1, 10 mM sodium phosphate, 90% H2O/10% D2O1H_sample90% H2O/10% D2O
solution20.2 mM [U-13C; U-15N] Ruminococcin C1, 10 mM sodium phosphate, 90% H2O/10% D2O15N13C_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMRuminococcin C1natural abundance1
10 mMsodium phosphatenatural abundance1
0.2 mMRuminococcin C1[U-13C; U-15N]2
10 mMsodium phosphatenatural abundance2
Sample conditions

Ionic strength: 10 mM / Ionic strength err: 0.1 / pH: 6.8 / PH err: 0.05 / Pressure: 1 bar / Temperature: 300 K / Temperature err: 0.1

Conditions-IDLabelPressure err
11H_sample
215N13C_sample0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
CYANA2.1Guntert P.structure calculation
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 5 / Details: steps : 60000
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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