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- PDB-2jos: Solution structure of piscidin in presence of DPC micelles -

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Basic information

Entry
Database: PDB / ID: 2jos
TitleSolution structure of piscidin in presence of DPC micelles
ComponentsMoronecidin
KeywordsANTIMICROBIAL PROTEIN / piscidin / antimicrobial / amphipathic helix / micellar environment
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
Biological speciesMorone saxatilis (striped sea-bass)
MethodSOLUTION NMR / distance geometry
AuthorsCampagna, S. / Saint, N. / Molle, G. / Aumelas, A.
CitationJournal: Biochemistry / Year: 2007
Title: Structure and mechanism of action of the antimicrobial peptide piscidin
Authors: Campagna, S. / Saint, N. / Molle, G. / Aumelas, A.
History
DepositionMar 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Source and taxonomy
Category: database_2 / diffrn ...database_2 / diffrn / diffrn_radiation / pdbx_entity_src_syn / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Moronecidin


Theoretical massNumber of molelcules
Total (without water)2,5791
Polymers2,5791
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 60structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Moronecidin / Piscidin-1


Mass: 2579.078 Da / Num. of mol.: 1 / Fragment: sequence database residues, 23-44 / Source method: obtained synthetically / Source: (synth.) Morone saxatilis (striped sea-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 DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1422D 1H-1H COSY
1522D 1H-1H TOCSY
1622D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM piscidin-1 in pure water, 90% H2O/10% D2Osample_190% H2O/10% D2O
micelle21 mM piscidin-1 in micellar environment, 90% H2O/10% D2Osample_290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMpiscidin-1natural abundance1
1 mMpiscidin-1natural abundance2
Sample conditionspH: 5.0 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert, Braun and Wuthrichstructure solution
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
XwinNMRBruker Biospinchemical shift assignment
DYANA1.5Guntert, Braun and Wuthrichrefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 60 / Conformers submitted total number: 10

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