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- PDB-2mag: NMR STRUCTURE OF MAGAININ 2 IN DPC MICELLES, 10 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 2mag
TitleNMR STRUCTURE OF MAGAININ 2 IN DPC MICELLES, 10 STRUCTURES
ComponentsMAGAININ 2
KeywordsANTIBIOTIC / MAGAININ / MEMBRANE / AMPHIPATHIC HELIX / MICELLE
Function / homologyregulation of defense response to virus / defense response to fungus / killing of cells of another organism / defense response to bacterium / innate immune response / extracellular region / Magainins
Function and homology information
Biological speciesXenopus laevis (African clawed frog)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsGesell, J.J. / Zasloff, M. / Opella, S.J.
CitationJournal: J.Biomol.NMR / Year: 1997
Title: Two-dimensional 1H NMR experiments show that the 23-residue magainin antibiotic peptide is an alpha-helix in dodecylphosphocholine micelles, sodium dodecylsulfate micelles, and trifluoroethanol/water solution.
Authors: Gesell, J. / Zasloff, M. / Opella, S.J.
History
DepositionDec 19, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 26, 2016Group: Structure summary
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: MAGAININ 2


Theoretical massNumber of molelcules
Total (without water)2,4701
Polymers2,4701
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50LOWEST ENERGY
Representative

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Components

#1: Protein/peptide MAGAININ 2 /


Mass: 2469.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE PEPTIDE WAS PREPARED BY SOLID-PHASE SYNTHESIS / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: P11006

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQF-COSY

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Sample preparation

Sample conditionspH: 4.1 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX600 / Manufacturer: Bruker / Model: DMX600 / Field strength: 600 MHz

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameVersionDeveloperClassification
X-PLOR INTERFACED THROUGH NMRCOMPASSNMRCOMPASSBRUNGERrefinement
BIOSYM NMRCOMPASSNMRCOMPASSstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 10

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