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- PDB-2kns: Helical Hairpin Structure of Pardaxin in Lipopolysaccharide Micel... -

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Basic information

Entry
Database: PDB / ID: 2kns
TitleHelical Hairpin Structure of Pardaxin in Lipopolysaccharide Micelles: Studied by NMR Spectroscopy
ComponentsPardaxin P-4
KeywordsANTIMICROBIAL PROTEIN / Pardaxin / Pa4 / LPS / trNOE / antimicrobial peptide / STD NMR / Ion transport / Porin / Secreted / Toxin / Transmembrane / Transport
Function / homologyPardaxin / Pardaxin / other organism cell membrane / monoatomic ion transport / toxin activity / extracellular region / membrane / Pardaxin P-4
Function and homology information
Biological speciesPardachirus marmoratus (finless sole)
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model 1
AuthorsBhunia, A. / Bhattacharjya, S. / Ramamoorthy, A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: NMR structure of pardaxin, a pore-forming antimicrobial peptide, in lipopolysaccharide Micelles: Mechanism of outer membrane permeabilization
Authors: Bhunia, A. / Domadia, P.N. / Torres, J. / Hallock, K.J. / Ramamoorthy, A. / Bhattacharjya, S.
History
DepositionSep 3, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 15, 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: Pardaxin P-4


Theoretical massNumber of molelcules
Total (without water)3,3261
Polymers3,3261
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 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Pardaxin P-4 / Pardaxin Pa4 / Pardaxin P1a


Mass: 3325.851 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Standard F-moc solid phase peptide synthesis / Source: (synth.) Pardachirus marmoratus (finless sole) / References: UniProt: P81861

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 0.5mM Pardaxin-1; 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: Pardaxin-1
Sample conditionspH: 4.5 / Temperature: 288 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: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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