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- PDB-9e3x: Backbone Modification in the Fungal Defensin Plectasin: Calpha-me... -

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Basic information

Entry
Database: PDB / ID: 9e3x
TitleBackbone Modification in the Fungal Defensin Plectasin: Calpha-methyl-residues in the helix
ComponentsFungal defensin plectasin variant NZ2114
KeywordsANTIMICROBIAL PROTEIN / plectasin derivative / defensin / antibiotic
Function / homology
Function and homology information


potassium channel regulator activity / toxin activity / defense response to bacterium / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Arthropod defensin / Invertebrate defensins family profile. / Defensin, invertebrate/fungal / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily
Similarity search - Domain/homology
Fungal defensin plectasin
Similarity search - Component
Biological speciesPseudoplectania nigrella (fungus)
MethodSOLUTION NMR / simulated annealing
AuthorsHarmon, T.W. / Song, J. / Gulewicz, A.J. / Di, Y.P. / Horne, W.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM149220 United States
CitationJournal: Chembiochem / Year: 2025
Title: Structural and Functional Mimicry of the Antimicrobial Defensin Plectasin by Analogues with Engineered Backbone Composition.
Authors: Harmon, T.W. / Song, J. / Gulewicz, A.J. / Di, Y.P. / Horne, W.S.
History
DepositionOct 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release
Revision 2.0Jan 15, 2025Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fungal defensin plectasin variant NZ2114


Theoretical massNumber of molelcules
Total (without water)4,4211
Polymers4,4211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: not applicable
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 Fungal defensin plectasin variant NZ2114


Mass: 4421.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudoplectania nigrella (fungus) / References: UniProt: Q53I06
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H COSY
131isotropic12D DQF-COSY
141isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 0.58 mM Heterogeneous-backbone analogue of plectasin variant NZ2114: alpha-Me-Leu13, Aib17, alpha-Me-Lys20, 20 mM [U-2H] sodium acetate, 0.13 mM 4,4-dimethyl-4-silapentane-1-ammonium ...Contents: 0.58 mM Heterogeneous-backbone analogue of plectasin variant NZ2114: alpha-Me-Leu13, Aib17, alpha-Me-Lys20, 20 mM [U-2H] sodium acetate, 0.13 mM 4,4-dimethyl-4-silapentane-1-ammonium trifluoroacetate (DSA), 90% H2O/10% D2O
Label: sample_1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.58 mMHeterogeneous-backbone analogue of plectasin variant NZ2114: alpha-Me-Leu13, Aib17, alpha-Me-Lys20natural abundance1
20 mMsodium acetate[U-2H]1
0.13 mM4,4-dimethyl-4-silapentane-1-ammonium trifluoroacetate (DSA)natural abundance1
Sample conditionsIonic strength: 29 mM / Label: conditions_1 / pH: 3.8 pH* / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leedata analysis
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leepeak picking
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
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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