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- PDB-7rul: I5R8 Mastoparano is a peptide synthetic, modified of Mastoparano ... -

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Basic information

Entry
Database: PDB / ID: 7rul
TitleI5R8 Mastoparano is a peptide synthetic, modified of Mastoparano (extracted from wasp venom)
ComponentsMastoparan-L peptide
KeywordsANTIVIRAL PROTEIN / antimicrobial
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
AuthorsAlves, E.S.F. / Santos, B.P.O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Mastoparan I5R8, peptide antiviral derived of Mastoparan, venenon vesp.
Authors: Alves, E.S.F. / Santos, B.P.O.
History
DepositionAug 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
A: Mastoparan-L peptide


Theoretical massNumber of molelcules
Total (without water)1,6091
Polymers1,6091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
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-L peptide


Mass: 1609.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vespula lewisii (insect) / Production host: Escherichia coli (E. coli) / 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: 2 mM I5R8, 100 mM [U-98% 2H] SDS-D25, 5 % v/v [U-98% 2H] DSS, 90% H2O/10% D2O
Details: A solution containing 2 mM of peptide was prepared in 100 mM of SDS-d25, 90:10 H2O/D2O and 5% of DSS, and the pH adjusted for 4.0.
Label: I5R8 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMI5R8natural abundance1
100 mMSDS-D25[U-98% 2H]1
5 % v/vDSS[U-98% 2H]1
Sample conditionsDetails: A solution containing 2 mM of peptide was prepared in 100 mM of SDS-d25, 90:10 H2O/D2O and 5% of DSS, and the pH adjusted for 4.0.
Ionic strength: neutral Not defined / Label: I5R8 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNdata analysis
ARIALinge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
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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