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- PDB-2n6m: Structural elucidation of the frog skin-derived peptide Esculenti... -

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Basic information

Entry
Database: PDB / ID: 2n6m
TitleStructural elucidation of the frog skin-derived peptide Esculentin-1a[Esc(1-21)NH2] inLipopolysaccharide and correlation with their function
ComponentsEsculentin-1A
KeywordsANTIMICROBIAL PROTEIN / Alpha helix / Antimicrobial Peptide / Anti endotoxin peptides / LPS
Function / homologyFrog antimicrobial peptide, brevinin-2/esculentin type / Frog antimicrobial peptide / killing of cells of another organism / defense response to bacterium / extracellular region / Esculentin-1A
Function and homology information
Biological speciesPelophylax esculentus (pool frog)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsGhosh, A. / Bhunia, A.
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: NMR structure and binding of esculentin-1a (1-21)NH2 and its diastereomer to lipopolysaccharide: Correlation with biological functions
Authors: Ghosh, A. / Bera, S. / Shai, Y. / Mangoni, M.L. / Bhunia, A.
History
DepositionAug 26, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
Revision 1.2May 15, 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: Esculentin-1A


Theoretical massNumber of molelcules
Total (without water)2,1911
Polymers2,1911
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 least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Esculentin-1A


Mass: 2190.736 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pelophylax esculentus (pool frog) / References: UniProt: P40843*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-1H NOESY

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Sample preparation

DetailsContents: 1 mM entity-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: entity-1
Sample conditionspH: 4.5 / Pressure: ambient / 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
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsProtein phi angle constraints total count: 20 / Protein psi angle constraints total count: 20
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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