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- PDB-2hfr: solution structure of antimicrobial peptide Fowlicidin 3 -

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Basic information

Entry
Database: PDB / ID: 2hfr
Titlesolution structure of antimicrobial peptide Fowlicidin 3
ComponentsFowlicidin-3
KeywordsANTIMICROBIAL PROTEIN / ALPHA HELIX
Function / homology
Function and homology information


disruption of plasma membrane integrity in another organism / lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / membrane => GO:0016020 / defense response to Gram-positive bacterium / negative regulation of gene expression / innate immune response / extracellular space
Similarity search - Function
MethodSOLUTION NMR / annealing
AuthorsBommineni, Y.R. / Dai, H. / Gong, Y. / Prakash, O. / Zhang, G.
Citation
Journal: Febs J. / Year: 2007
Title: Fowlicidin-3 is an alpha-helical cationic host defense peptide with potent antibacterial and lipopolysaccharide-neutralizing activities.
Authors: Bommineni, Y.R. / Dai, H. / Gong, Y.X. / Soulages, J.L. / Fernando, S.C. / Desilva, U. / Prakash, O. / Zhang, G.
#1: Journal: Eur.J.Biochem. / Year: 2006
Title: Structure activity relationships of fowlicidin-1, a cathelicidin antimicrobial peptide in chicken
Authors: Xiao, Y. / Dai, H. / Bommineni, Y.R. / Soulages, J.L. / Gong, Y. / Prakash, O. / Zhang, G.
History
DepositionJun 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 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: 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 1.4May 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: Fowlicidin-3


Theoretical massNumber of molelcules
Total (without water)3,1021
Polymers3,1021
Non-polymers00
Water0
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Fowlicidin-3 / cathelicidin


Mass: 3101.777 Da / Num. of mol.: 1 / Fragment: residues 125-151 / Source method: obtained synthetically
Details: This sequence occurs naturally in Gallus gallus (chicken).
References: UniProt: Q2IAL6

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 4mM Fowlicidin 3, 50%TFE, 50%H2O / Solvent system: 50%TFE, 50%H2O
Sample conditionspH: 6.0 / 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
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: annealing / Software ordinal: 1 / Details: 205 NOE constraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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