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- PDB-1f0f: Cecropin A(1-8)-magainin 2(1-12) gig deletion modification in dod... -

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Entry
Database: PDB / ID: 1f0f
TitleCecropin A(1-8)-magainin 2(1-12) gig deletion modification in dodecylphosphocholine micelles
ComponentsCECROPIN A-MAGAININ 2 HYBRID PEPTIDE
KeywordsANTITUMOR PROTEIN / Helix
Function / homology
Function and homology information


antimicrobial peptide biosynthetic process / extraorganismal space / regulation of defense response to virus / defense response to fungus / antibacterial humoral response / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / innate immune response / extracellular region
Similarity search - Function
Cecropin family signature. / Cecropin / Cecropin family
Similarity search - Domain/homology
Cecropin-A / Magainins
Similarity search - Component
MethodSOLUTION NMR / Distance Geometry-Dynamical Simulated Annealing Hybrid Method
AuthorsOh, D. / Shin, S.Y. / Lee, S. / Kim, Y.
CitationJournal: Biochemistry / Year: 2000
Title: Role of the hinge region and the tryptophan residue in the synthetic antimicrobial peptides, cecropin A(1-8)-magainin 2(1-12) and its analogues, on their antibiotic activities and structures.
Authors: Oh, D. / Shin, S.Y. / Lee, S. / Kang, J.H. / Kim, S.D. / Ryu, P.D. / Hahm, K.S. / Kim, Y.
History
DepositionMay 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2000Provider: 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CECROPIN A-MAGAININ 2 HYBRID PEPTIDE


Theoretical massNumber of molelcules
Total (without water)2,1841
Polymers2,1841
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)20 / 50structures with the lowest energy
Representative

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Components

#1: Protein/peptide CECROPIN A-MAGAININ 2 HYBRID PEPTIDE


Mass: 2183.789 Da / Num. of mol.: 1 / Mutation: GIG DELETION IN MAGAININ SEGMENT / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE FOR THIS PEPTIDE IS A HYBRID OF SEQUENCES WHICH OCCUR NATURALLY IN HYALOPHORA CECROPIA (CECROPIA MOTH) AND XENOPUS LAEVIS (AFRICAN CLAWED FROG)
References: UniProt: P01507, UniProt: P11006
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: DODECYLPHOSPHOCHOLINE-d38 MICELLES / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 4.29 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 400 MHz

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Processing

NMR softwareName: X-PLOR / Version: 3.851 / Developer: Brunger, A.T. / Classification: refinement
RefinementMethod: Distance Geometry-Dynamical Simulated Annealing Hybrid Method
Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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