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- PDB-2mcv: Solid-state NMR structure of piscidin 1 in aligned 1:1 phosphatid... -

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Basic information

Entry
Database: PDB / ID: 2mcv
TitleSolid-state NMR structure of piscidin 1 in aligned 1:1 phosphatidylethanolamine/phosphoglycerol lipid bilayers
ComponentsMoronecidin
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptide / anticancer peptide / anti HIV-1 / cationic / amphipathic / histidine rich / helical / lipid bilayers / bacterial cell membrane mimic
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)
MethodSOLID-STATE NMR / simulated annealing
Model detailslowest energy, model1
AuthorsFu, R. / Tian, Y. / Perrin Jr., B.S. / Grant, C.V. / Hayden, R.M. / Pastor, R.W. / Cotten, M.L.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: High-resolution structures and orientations of antimicrobial peptides piscidin 1 and piscidin 3 in fluid bilayers reveal tilting, kinking, and bilayer immersion.
Authors: Perrin, B.S. / Tian, Y. / Fu, R. / Grant, C.V. / Chekmenev, E.Y. / Wieczorek, W.E. / Dao, A.E. / Hayden, R.M. / Burzynski, C.M. / Venable, R.M. / Sharma, M. / Opella, S.J. / Pastor, R.W. / Cotten, M.L.
History
DepositionAug 27, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
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_ref_seq_dif.details

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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)2,5771
Polymers2,5771
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Moronecidin / Piscidin-1


Mass: 2577.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct / Source: (synth.) Morone saxatilis (striped sea-bass) / References: UniProt: Q8UUG0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experimentType: 15N 1H solid-state de-HETCOR

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Sample preparation

DetailsContents: 15-20 MM PISCIDIN 1, 300-400 MM 1:1 (MOLAR) 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-PHOSPHATIDYLETHANOLAMINE/1-PALMITOYL-2-OLEOYL-SN-GLYCERO-PHOSPHOGLYCEROL, 40 MM PHOSPHATE BUFFER WITH 100% H2O
Solvent system: 100% H2O
Sample conditionspH: 6 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
Xplor-NIHBrunger A. T. et.al.structure solution
Xplor-NIHBrunger A. T. et.al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structures were calculated using a simulated annealing protocol within Xplor-NIH with torsion angle molecular dynamics in the presence of experimentally determined restraints. Solid-state ...Details: Structures were calculated using a simulated annealing protocol within Xplor-NIH with torsion angle molecular dynamics in the presence of experimentally determined restraints. Solid-state NMR experiments on static oriented lipid bilayer samples allowed for the measurements of anisotropic backbone 15N chemical shifts and 15N-1H dipolar couplings, which were used as the experimental restraints. The initial structure was an alpha helix with ideal phi/psi angles (-61/-45). The calculations also included the Xplor-NIH potential for knowledge-based torsion angles and the routine terms ANGL, BOND and IMPR. A total of 100 structures were generated and the 10 lowest energy structures were accepted for analysis and representation. By convention, the bilayer normal for all of the oriented samples is aligned along the z-axis of the calculated structures.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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