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- PDB-2n5w: The NMR solution structure of octyl-tridecaptin A1 in DPC micelles -

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Basic information

Entry
Database: PDB / ID: 2n5w
TitleThe NMR solution structure of octyl-tridecaptin A1 in DPC micelles
ComponentsOctyl-tridecaptin A1
KeywordsANTIMICROBIAL PROTEIN / Tridecaptin A1 / Lipopeptide / Antimicrobial / Antibiotic / Non-ribosomal
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model1
AuthorsCochrane, S.A. / Findlay, B. / Bakhtiary, A. / Acedo, J.Z. / Rodriguez-Lopez, E.M. / Vederas, J.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Antimicrobial lipopeptide tridecaptin A1 selectively binds to Gram-negative lipid II.
Authors: Cochrane, S.A. / Findlay, B. / Bakhtiary, A. / Acedo, J.Z. / Rodriguez-Lopez, E.M. / Mercier, P. / Vederas, J.C.
History
DepositionAug 1, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Oct 26, 2016Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Octyl-tridecaptin A1


Theoretical massNumber of molelcules
Total (without water)1,5211
Polymers1,5211
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Octyl-tridecaptin A1


Mass: 1520.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Fmoc-SPPS synthesis

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The NMR solution structure of octyl-tridecaptin A1 in DPC micelles. The N-terminal lipid tail was omitted in the structure calculation.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 180 mM DPC, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 180 mM / Component: DPC-1
Sample conditionspH: 6 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR softwareName: CYANA / Developer: Guntert P. / Classification: refinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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