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- PDB-1d7n: SOLUTION STRUCTURE ANALYSIS OF THE MASTOPARAN WITH DETERGENTS -

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Basic information

Entry
Database: PDB / ID: 1d7n
TitleSOLUTION STRUCTURE ANALYSIS OF THE MASTOPARAN WITH DETERGENTS
ComponentsPROTEIN (WASP VENOM PEPTIDE (MASTOPARAN))
KeywordsTOXIN / SODIUM DODECYL SULFATE BOUND CONFORMATION / IMMUNE SYSTEM
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
AuthorsHori, Y. / Demura, M. / Iwadate, M. / Niidome, T. / Aoyagi, H. / Asakura, T.
CitationJournal: Eur.J.Biochem. / Year: 2001
Title: Interaction of mastoparan with membranes studied by 1H-NMR spectroscopy in detergent micelles and by solid-state 2H-NMR and 15N-NMR spectroscopy in oriented lipid bilayers.
Authors: Hori, Y. / Demura, M. / Iwadate, M. / Ulrich, A.S. / Niidome, T. / Aoyagi, H. / Asakura, T.
History
DepositionOct 19, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (WASP VENOM PEPTIDE (MASTOPARAN))


Theoretical massNumber of molelcules
Total (without water)1,4811
Polymers1,4811
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 least restraint violations
Representative

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Components

#1: Protein/peptide PROTEIN (WASP VENOM PEPTIDE (MASTOPARAN))


Mass: 1480.923 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vespula lewisii (insect) / Secretion: VENOM / References: UniProt: P01514

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY

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Sample preparation

DetailsContents: 5MM MASTOPARAN SODIUM DODECYL SULFATE- D25; 90% H2O, 10% D2O
Sample conditionsPressure: AMBIENT / Temperature: 303.15 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: JEOL A / Manufacturer: JEOL / Model: A / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
DGII MSI NMRCHITECT 95.0MSIrefinement
DGII MSIMSIstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 94 NOE-DERIVED DISTANCE CONSTRAINTS.
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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