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- PDB-6v1n: CSP1-E1A-cyc(Dap6E10) -

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Basic information

Entry
Database: PDB / ID: 6v1n
TitleCSP1-E1A-cyc(Dap6E10)
ComponentsCompetence-stimulating peptide type 1
KeywordsBIOSYNTHETIC PROTEIN / modulator / quorum sensing
Function / homologyCompetence protein, ComC / COMC family / pheromone activity / establishment of competence for transformation / extracellular region / Competence-stimulating peptide type 1
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsYang, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Science Foundation (NSF, United States) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Designing cyclic competence-stimulating peptide (CSP) analogs with pan-group quorum-sensing inhibition activity inStreptococcus pneumoniae.
Authors: Yang, Y. / Lin, J. / Harrington, A. / Cornilescu, G. / Lau, G.W. / Tal-Gan, Y.
History
DepositionNov 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 2, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Competence-stimulating peptide type 1


Theoretical massNumber of molelcules
Total (without water)2,1611
Polymers2,1611
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Competence-stimulating peptide type 1 / CSP-1


Mass: 2160.653 Da / Num. of mol.: 1 / Mutation: E1A, K6(DPP), D10E / Source method: obtained synthetically
Details: DPP and GLU were chemically added to the 6th and 10th positions and then cyclized. However, during structure calculation, GLU10 was labeled as GLN10 to construct the macrocycle for ...Details: DPP and GLU were chemically added to the 6th and 10th positions and then cyclized. However, during structure calculation, GLU10 was labeled as GLN10 to construct the macrocycle for convenience. GLN10 was kept in the final coordinate file and chemical shift file for consistency. The actual sequence is still: AMRLS(DPP)FFR(GLU)FILQRKK
Source: (synth.) Streptococcus pneumoniae (bacteria) / References: UniProt: P60242
Has ligand of interestY
Has protein modificationY
Sequence detailsDPP and GLU were chemically added to the 6th and 10th positions and then cyclized. However, during ...DPP and GLU were chemically added to the 6th and 10th positions and then cyclized. However, during structure calculation, GLU10 was labeled as GLN10 to construct the macrocycle for convenience. GLN10 was kept in the final coordinate file and chemical shift file for consistency. The actual sequence is still: AMRLS(DPP)FFR(GLU)FILQRKK

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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 COSY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-13C HSQC
151isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 1.9 mM CSP1-E1A-cyc(Dap6E10), 250 mM deuterium DPC, 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM Na2HPO4, 1.8 mM KH2PO4, 90% H2O/10% D2O
Label: 1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.9 mMCSP1-E1A-cyc(Dap6E10)natural abundance1
250 mMDPCdeuterium1
137 mMsodium chloridenatural abundance1
2.7 mMpotassium chloridenatural abundance1
10 mMNa2HPO4natural abundance1
1.8 mMKH2PO4natural abundance1
Sample conditionsIonic strength: 0.15 M / Label: 1 / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSCHWIETERSrefinement
X-PLOR NIHKUSZEWSKIrefinement
Sparkystructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: WITH EEFX REFINEMENT
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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