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- PDB-6r96: The solution NMR structure of cis-dicarba-brevinin-1BYa in sodium... -

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Basic information

Entry
Database: PDB / ID: 6r96
TitleThe solution NMR structure of cis-dicarba-brevinin-1BYa in sodium dodecyl sulphate micelles
ComponentsBrevinin-1BYa
KeywordsANTIMICROBIAL PROTEIN / cationic / rana-box / 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.
#2: Journal: Eur. Biophys. J. / Year: 2011
Title: Synthesis, conformational analysis and biological properties of a dicarba derivative of the antimicrobial peptide, brevinin-1BYa.
Authors: Hossain, M.A. / Guilhaudis, L. / Sonnevend, A. / Attoub, S. / van Lierop, B.J. / Robinson, A.J. / Wade, J.D. / Conlon, J.M.
History
DepositionApr 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Brevinin-1BYa


Theoretical massNumber of molelcules
Total (without water)2,5771
Polymers2,5771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NA
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2350 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1medoid

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Components

#1: Protein/peptide Brevinin-1BYa


Mass: 2577.240 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: AGL = allylglycine An intramolecular vinylic bond exists between the residues AGL-18 and AGL-24.
Source: (synth.) Rana boylii (yellow-legged frog) / References: UniProt: P84111
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: micelle
Contents: 1.5 mM NA- dicarba-brevinin-1BYa, 230 mM sodium dodecyl sulfphate, 90% H2O/10% D2O
Details: Sodium dodecyl sulphate micelles / Label: sample_1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMdicarba-brevinin-1BYaNA-1
230 mMsodium dodecyl sulfphatenatural abundance1
Sample conditionsIonic strength: 0 Not defined / Label: conditions_1 / pH: 7.0 Not defined / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
NAMDUNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGNrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRFAM-SPARKYNMRFAMchemical shift assignment
NMRFAM-SPARKYNMRFAMpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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