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- PDB-8ep5: Solution NMR structure of a computationally designed mastoparan-l... -

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Basic information

Entry
Database: PDB / ID: 8ep5
TitleSolution NMR structure of a computationally designed mastoparan-like peptide, mastoparan-R1
ComponentsMastoparan-R1 peptide
KeywordsANTIMICROBIAL PROTEIN / Antimicrobial Peptide / AMPs
Function / homology
Function and homology information


other organism cell membrane / defense response to fungus / toxin activity / killing of cells of another organism / defense response to bacterium / innate immune response / extracellular region / membrane
Similarity search - Function
Mastoparan / Mastoparan protein
Similarity search - Domain/homology
Biological speciesVespula lewisii (insect)
MethodSOLUTION NMR / simulated annealing
AuthorsFreitas, C.D.P. / Oshiro, K.G.N. / Macedo, M.L.R. / Cardoso, M.H. / Franco, O.L. / Liao, L.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: To Be Published
Title: Solution NMR structure of a computationally designed mastoparan-like peptide, mastoparan-R1.
Authors: Freitas, C.D.P. / Oshiro, K.G.N. / Macedo, M.L.R. / Cardoso, M.H. / Franco, O.L. / Liao, L.M.
History
DepositionOct 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Mastoparan-R1 peptide


Theoretical massNumber of molelcules
Total (without water)1,6401
Polymers1,6401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area110 Å2
ΔGint1 kcal/mol
Surface area1730 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Mastoparan-R1 peptide


Mass: 1640.218 Da / Num. of mol.: 1 / Mutation: I1K, N2I, A5R, L9K, A10I / Source method: obtained synthetically / Source: (synth.) Vespula lewisii (insect) / References: UniProt: P01514
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 NOESY
131isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 1.5 mM Mastoparan-R1, 75 mM [U-98% 2H] SDS-d25, 0.05 % [U-98% 2H] DSS-d6, 90% H2O/10% D2O
Label: Mastoparan-R1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMMastoparan-R1natural abundance1
75 mMSDS-d25[U-98% 2H]1
0.05 %DSS-d6[U-98% 2H]1
Sample conditionsIonic strength: acid Not defined / Label: Mastoparan_R1 / pH: 4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.5.2CCPNchemical shift assignment
ARIA2.3.2Linge, O'Donoghue and Nilgesstructure calculation
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNpeak picking
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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