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- PDB-2g9l: The High-resolution Solution Conformation of an Antimicrobial Pep... -

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Basic information

Entry
Database: PDB / ID: 2g9l
TitleThe High-resolution Solution Conformation of an Antimicrobial Peptide Gaegurin 4 and Its Mode of Membrane Interaction
ComponentsGaegurin-4
KeywordsANTIBIOTIC / amphipathic helix
Function / homologyFrog antimicrobial peptide, brevinin-2/esculentin type / Frog antimicrobial peptide / Frog antimicrobial peptide, propeptide / Frog skin active peptide family signal and propeptide / EF-Hand 1, calcium-binding site / defense response to bacterium / extracellular region / Gaegurin-4
Function and homology information
MethodSOLUTION NMR / distance geometry, molecular dynamics
AuthorsChi, S.-W. / Han, K.-H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: Solution structure and membrane interaction mode of an antimicrobial peptide gaegurin 4
Authors: Chi, S.-W. / Kim, J.-S. / Kim, D.-H. / Lee, S.-H. / Park, Y.-H. / Han, K.-H.
History
DepositionMar 6, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gaegurin-4


Theoretical massNumber of molelcules
Total (without water)3,7551
Polymers3,7551
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)15 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Gaegurin-4 / ggn4


Mass: 3755.494 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence occurs naturally found in Korean frog, Rana rugosa.
References: UniProt: P80398
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
2412D NOESY
2512D TOCSY
261DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2mM ggn4, 80% CD3OH, 20% H2O / Solvent system: 80% CD3OH, 20% H2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1041 atm298 K
2041 atm283 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionClassification
VNMR6.1Bcollection
Felix98processing
Discover2.98refinement
RefinementMethod: distance geometry, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 15

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