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- PDB-6dul: Three-Dimensional Structures for mastoparano-L -

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Basic information

Entry
Database: PDB / ID: 6dul
TitleThree-Dimensional Structures for mastoparano-L
Componentsmastoparano-L
KeywordsTOXIN / Three-dimensional structure / SDS micelles / PAM.
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. / Rodriguez, L.V. / Liao, L.M.
CitationJournal: To Be Published
Title: Three-Dimensional Structures for mastoparano-L
Authors: Alves, E.S.F. / Rodriguez, L.V. / Liao, L.M.
History
DepositionJun 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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 / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mastoparano-L


Theoretical massNumber of molelcules
Total (without water)1,4811
Polymers1,4811
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
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 mastoparano-L


Mass: 1480.923 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This peptide is a potent stimulator of exocytosis of various mammalian cells.
Source: (synth.) Vespula lewisii (insect) / References: UniProt: P01514*PLUS
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
141isotropic12D 1H-13C HMQC

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Sample preparation

DetailsType: solution
Contents: 1 mM mastoparano-L, 100 mM [U-98% 2H] SDS-d25, 5 % v/v [U-98% 2H] TMSP-d4, 90 % v/v H2O, 10 % v/v [U-99% 2H] D2O, 90% H2O/10% D2O
Label: mastoparano-L / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMmastoparano-Lnatural abundance1
100 mMSDS-d25[U-98% 2H]1
5 % v/vTMSP-d4[U-98% 2H]1
90 % v/vH2Onatural abundance1
10 % v/vD2O[U-99% 2H]1
Sample conditionsIonic strength: acid Not defined / Label: mastoparano-L / 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
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
TALOSCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1
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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