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- PDB-2ojm: Solution structure and cell selectivity of Piscidin 1 and its ana... -

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Basic information

Entry
Database: PDB / ID: 2ojm
TitleSolution structure and cell selectivity of Piscidin 1 and its analogues
ComponentsMoronecidin
KeywordsANTIMICROBIAL PROTEIN / Piscidin 1 / antimicrobial peptide / proline / membrane
Function / homologyPleurocidin / Pleurocidin family / defense response to fungus / killing of cells of another organism / defense response to bacterium / extracellular region / Moronecidin
Function and homology information
MethodSOLUTION NMR
AuthorsLee, S.A. / Kim, Y.K. / Kim, Y.
CitationJournal: Biochemistry / Year: 2007
Title: Solution structure and cell selectivity of piscidin 1 and its analogues.
Authors: Lee, S.A. / Kim, Y.K. / Lim, S.S. / Zhu, W.L. / Ko, H. / Shin, S.Y. / Hahm, K.S. / Kim, Y.
History
DepositionJan 12, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Moronecidin


Theoretical massNumber of molelcules
Total (without water)2,5791
Polymers2,5791
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 Moronecidin / Piscidin-1


Mass: 2579.078 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in hybrid striped bass
References: UniProt: Q8UUG0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY

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Sample preparation

DetailsContents: 1.5mM Piscidin 1; 300mM SDS micelles; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 4.12 / Pressure: ambient / Temperature: 318 K

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Frank Delaglioprocessing
X-PLOR3.851structure solution
X-PLOR3.851refinement
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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