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- PDB-2mhw: The solution NMR structure of maximin-4 in SDS micelles -

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Basic information

Entry
Database: PDB / ID: 2mhw
TitleThe solution NMR structure of maximin-4 in SDS micelles
ComponentsAntimicrobial peptide
KeywordsANTIMICROBIAL PROTEIN / MEMBRANE PROTEIN / membrane peptides / lipid bilayers / bacterial resistance / antimicrobial peptides
Function / homologyBombinin / Bombinin / defense response to fungus / killing of cells of another organism / defense response to bacterium / extracellular region / Antimicrobial peptide / Maximins 4/H3 type 3
Function and homology information
Biological speciesBombina maxima (large-webbed bell toad)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model1
AuthorsToke, O. / Banoczi, Z. / Kiraly, P. / Heinzmann, R. / Burck, J. / Ulrich, A.S. / Hudecz, F.
CitationJournal: Eur.Biophys.J. / Year: 2011
Title: A kinked antimicrobial peptide from Bombina maxima. I. Three-dimensional structure determined by NMR in membrane-mimicking environments.
Authors: Toke, O. / Banoczi, Z. / Kiraly, P. / Heinzmann, R. / Burck, J. / Ulrich, A.S. / Hudecz, F.
History
DepositionDec 5, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antimicrobial peptide


Theoretical massNumber of molelcules
Total (without water)2,6171
Polymers2,6171
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Antimicrobial peptide


Mass: 2617.137 Da / Num. of mol.: 1 / Fragment: UNP residues 44-70 / Source method: obtained synthetically / Source: (synth.) Bombina maxima (large-webbed bell toad) / References: UniProt: C3RSY7, UniProt: Q58T52*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D 1H-15N HSQC
1412D 1H-13C HSQC

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Sample preparation

DetailsContents: 1-1.2 mM maximin, 10 mM sodium-phosphate, 200 mM [U-100% 2H] d25-sodium-dodecyl-sulfate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMmaximin-4-11-1.21
10 mMsodium-phosphate-21
200 mMd25-sodium-dodecyl-sulfate-3[U-100% 2H]1
Sample conditionsIonic strength: 220 / pH: 5 / Pressure: ambient / Temperature: 313 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
FelixAccelryspeak picking
FelixAccelrysprocessing
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
ARIALinge, O'Donoghue and Nilgesgeometry optimization
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
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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