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- PDB-5xdj: Esculentin-1a(1-21)NH2 -

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Basic information

Entry
Database: PDB / ID: 5xdj
TitleEsculentin-1a(1-21)NH2
ComponentsEsculentin-1A
KeywordsANTIMICROBIAL PROTEIN / Antimicrobial Peptides
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 / DGSA-distance geometry simulated annealing
AuthorsGhosh, A. / Bhunia, A.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Membrane perturbing activities and structural properties of the frog-skin derived peptide Esculentin-1a(1-21)NH2 and its Diastereomer Esc(1-21)-1c: Correlation with their antipseudomonal and cytotoxic activity
Authors: Loffredo, M.R. / Ghosh, A. / Harmouche, N. / Casciaro, B. / Luca, V. / Bortolotti, A. / Cappiello, F. / Stella, L. / Bhunia, A. / Bechinger, B. / Mangoni, M.L.
History
DepositionMar 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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 / _pdbx_nmr_spectrometer.model
Revision 1.3May 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_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2150 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Esculentin-1A


Mass: 2190.736 Da / Num. of mol.: 1 / Fragment: UNP residues 1-21 / Mutation: N21G / Source method: obtained synthetically / Source: (synth.) Pelophylax esculentus (pool frog) / References: UniProt: P40843

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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: 1.0 mM Esculentin-1a, 55.55 M H2O, 125 mM d38-DPC, 90% H2O/10% D2O
Label: peptide / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMEsculentin-1anatural abundance1
55.55 MH2Onatural abundance1
125 mMd38-DPCnatural abundance1
Sample conditionsIonic strength: 55.5 M / Label: condition_1 / pH: 4.5 / PH err: 0.1 / Pressure: 1013.25 mbar mbar / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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