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- PDB-2gdl: Fowlicidin-2: NMR structure of antimicrobial peptide -

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Basic information

Entry
Database: PDB / ID: 2gdl
TitleFowlicidin-2: NMR structure of antimicrobial peptide
Componentsmyeloid antimicrobial peptide 27
KeywordsANTIMICROBIAL PROTEIN / ANTIMICROBIAL PEPTIDE / CATHELICIDIN / ALPHA HELIX
Function / homology:
Function and homology information
MethodSOLUTION NMR / distance geometry simulated annealing
Model type detailsminimized average
AuthorsHerrera, A.I. / Prakash, O. / Zhang, G.
CitationJournal: To be Published
Title: The Central Kink Region of alpha-Helical Fowlicidin-2 is Critically Involved in Antibacterial and Lipopolysaccharide-Neutralizing Activities
Authors: Herrera, A. / Xiao, Y. / Soulages, J.L. / Bommineni, Y.R. / Prakash, O. / Zhang, G.
History
DepositionMar 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 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 / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 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: myeloid antimicrobial peptide 27


Theoretical massNumber of molelcules
Total (without water)3,7721
Polymers3,7721
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)9 / 100structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide myeloid antimicrobial peptide 27


Mass: 3771.562 Da / Num. of mol.: 1 / Fragment: residues 123-153 / Source method: obtained synthetically
Details: This sequence occurs naturally in Gallus gallus (chicken)
References: GenBank: 60459251

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 3mM Fowlicidin-2, 50% deuterated trifluoroethanol, 50% H2O
Solvent system: 50% H2O/50% D2O
Sample conditionsIonic strength: 100 mM / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1 Ccollection
Sparky3.11Goddard, T.D. and Kneller, D.G.data analysis
CNS1.1Brunger et al.structure solution
SYBYL7.1refinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 9

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