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- PDB-6g4v: The solution NMR structure of [C18S,C24S]brevinin-1BYa in 33% tri... -

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Basic information

Entry
Database: PDB / ID: 6g4v
TitleThe solution NMR structure of [C18S,C24S]brevinin-1BYa in 33% trifluoroethanol
Components[C18S,C24S]brevinin-1BYa
KeywordsANTIMICROBIAL PROTEIN / cationic / antimicrobial peptide
Function / homologyFrog antimicrobial peptide, brevinin-1 type / Frog antimicrobial peptide / defense response to fungus / killing of cells of another organism / defense response to bacterium / extracellular region / Brevinin-1BYa
Function and homology information
Biological speciesRana boylii (yellow-legged frog)
MethodSOLUTION NMR / simulated annealing
AuthorsTimmons, P.B. / O'Flynn, D.P. / Conlon, J.M. / Hewage, C.M.
Citation
Journal: Eur.Biophys.J. / Year: 2019
Title: Insights into conformation and membrane interactions of the acyclic and dicarba-bridged brevinin-1BYa antimicrobial peptides.
Authors: Timmons, P.B. / O'Flynn, D. / Conlon, J.M. / Hewage, C.M.
#1: Journal: J. Pept. Res. / Year: 2003
Title: Isolation of peptides of the brevinin-1 family with potent candidacidal activity from the skin secretions of the frog Rana boylii.
Authors: Conlon, J.M. / Sonnevend, A. / Patel, M. / Davidson, C. / Nielsen, P.F. / Pal, T. / Rollins-Smith, L.A.
History
DepositionMar 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Structure summary / Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _entity.pdbx_description
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: [C18S,C24S]brevinin-1BYa


Theoretical massNumber of molelcules
Total (without water)2,5811
Polymers2,5811
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2630 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1medoid

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Components

#1: Protein/peptide [C18S,C24S]brevinin-1BYa


Mass: 2581.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rana boylii (yellow-legged frog) / References: UniProt: P84111

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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: 1.5 mM NA- [C18S,C24S]brevinin-1BYa, trifluoroethanol/water
Label: sample_1 / Solvent system: trifluoroethanol/water
SampleConc.: 1.5 mM / Component: [C18S,C24S]brevinin-1BYa / Isotopic labeling: NA-
Sample conditionsIonic strength: 0 Not defined / Label: conditions_1 / pH: 7 / Pressure: 100000 Pa / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE DRX / Manufacturer: Bruker / Model: AVANCE DRX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert P.structure calculation
NMRFAM-SPARKYNATIONAL MAGNETIC RESONANCE FACILITY AT MADISONpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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