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- PDB-2k98: Helical hairpin structure of potent antimicrobial peptide MSI-594... -

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Entry
Database: PDB / ID: 2k98
TitleHelical hairpin structure of potent antimicrobial peptide MSI-594 in the presence of Lipopolysaccharide micelle
ComponentsMSI-594
KeywordsANTIMICROBIAL PROTEIN / MSI-594 / LPS / trNOE / antimicrobial peptide
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsBhunia, A. / Bhattacharjya, S. / Ramamoorthy, A.
CitationJournal: Chemistry / Year: 2009
Title: Helical Hairpin Structure of a Potent Antimicrobial Peptide MSI-594 in Lipopolysaccharide Micelles by NMR Spectroscopy
Authors: Bhunia, A. / Ramamoorthy, A. / Bhattacharjya, S.
History
DepositionSep 30, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 29, 2024Group: 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: MSI-594


Theoretical massNumber of molelcules
Total (without water)2,4471
Polymers2,4471
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 MSI-594


Mass: 2447.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Standard F-moc solid phase peptide synthesis

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H trNOESY
NMR detailsText: The structure was determined using tr-NOE data

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Sample preparation

DetailsContents: 0.5mM MSI-594, 0.13mg/mL LPS, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.5 mMMSI-5941
0.13 mg/mLLPS1
Sample conditionspH: 4.5 / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR softwareName: DYANA / Version: 1.5 / Developer: Guntert, Braun and Wuthrich / Classification: refinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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