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- PDB-1dum: NMR STRUCTURE OF [F5Y, F16W] MAGAININ 2 BOUND TO PHOSPHOLIPID VESICLES -

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Basic information

Entry
Database: PDB / ID: 1dum
TitleNMR STRUCTURE OF [F5Y, F16W] MAGAININ 2 BOUND TO PHOSPHOLIPID VESICLES
ComponentsMAGAININ 2
KeywordsANTIMICROBIAL PROTEIN / antibiotic / magainin / dimer / amphipathic helix / membrane / vesicle / bilayer
Function / homologyantimicrobial peptide biosynthetic process / extraorganismal space / regulation of defense response to virus / defense response to fungus / killing of cells of another organism / defense response to bacterium / innate immune response / Magainins
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsTakeda, A. / Wakamatsu, K. / Tachi, T. / Matsuzaki, K.
CitationJournal: Biopolymers / Year: 2001
Title: Effects of peptide dimerization on pore formation: Antiparallel disulfide-dimerized magainin 2 analogue.
Authors: Hara, T. / Kodama, H. / Kondo, M. / Wakamatsu, K. / Takeda, A. / Tachi, T. / Matsuzaki, K.
History
DepositionJan 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 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: MAGAININ 2
B: MAGAININ 2


Theoretical massNumber of molelcules
Total (without water)5,0542
Polymers5,0542
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide MAGAININ 2


Mass: 2526.973 Da / Num. of mol.: 2 / Mutation: F5Y, F16W / Source method: obtained synthetically
Details: The peptide was prepared by solid-phase synthesis. The sequence of this peptide naturally occurs in Xenopus laevis (African clawed frog)
References: UniProt: P11006

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 5mM [F5Y, F16W] magainin 2, 0.5mM DLPC-d64 / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50mM / pH: 5.2 / Pressure: ambient / Temperature: 318 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker ARX / Manufacturer: Bruker / Model: ARX / Field strength: 400 MHz

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR1.3Brukercollection
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 466 NOE-derived distance constraints (per protomer), 32 of which are treated as ambiguous.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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