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- PDB-6cj8: CSP1 -

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Basic information

Entry
Database: PDB / ID: 6cj8
TitleCSP1
ComponentsCompetence-stimulating peptide type 1
KeywordsSIGNALING PROTEIN / pneumococcus / quorum sensing / signaling molecule / CSP
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 / torsion angle dynamics
AuthorsYang, Y.
CitationJournal: Biochemistry / Year: 2018
Title: Structural Characterization of Competence-Stimulating Peptide Analogues Reveals Key Features for ComD1 and ComD2 Receptor Binding in Streptococcus pneumoniae.
Authors: Yang, Y. / Cornilescu, G. / Tal-Gan, Y.
History
DepositionFeb 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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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)2,2491
Polymers2,2491
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: manually synthesized as linear peptide
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1920 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

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


Mass: 2248.735 Da / Num. of mol.: 1 / Fragment: UNP residues 25-41 / Source method: obtained synthetically / Source: (synth.) Streptococcus pneumoniae (bacteria) / References: UniProt: P60242

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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-15N HSQC
151isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution / Contents: 250 mM D DPC, 1.9 mM CSP1, 90% H2O/10% D2O / Label: 1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
250 mMDPCD1
1.9 mMCSP1natural abundance1
Sample conditionsIonic strength: 0.15 M / Label: 1 / pH: 7.4 / Pressure: ambient 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
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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