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- PDB-2rlh: NMR structure of the antimicrobial peptide RP-1 bound to DPC micelles -

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Entry
Database: PDB / ID: 2rlh
TitleNMR structure of the antimicrobial peptide RP-1 bound to DPC micelles
Componentsantimicrobial peptide RP-1
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptide / alpha-helix / amphipathic / micelle
MethodSOLUTION NMR / simulated annealing
AuthorsBourbigot, S. / Dodd, E. / Horwood, C. / Booth, V.
CitationJournal: Biopolymers / Year: 2009
Title: Antimicrobial peptide RP-1 structure and interactions with anionic versus zwitterionic micelles.
Authors: Bourbigot, S. / Dodd, E. / Horwood, C. / Cumby, N. / Fardy, L. / Welch, W.H. / Ramjan, Z. / Sharma, S. / Waring, A.J. / Yeaman, M.R. / Booth, V.
History
DepositionJul 7, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: antimicrobial peptide RP-1


Theoretical massNumber of molelcules
Total (without water)2,1711
Polymers2,1711
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 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide antimicrobial peptide RP-1


Mass: 2170.812 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: solid phase synthesis employing Fmoc (O-fluorenylmethyl-oxycarbonyl) chemistry

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 1.5mM [U-15N]-Leu protein, 0.4mM DSS, 150mM [U-99% 2H] DPC, 0.4mM sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMprotein[U-15N]-Leu1
0.4 mMDSS1
150 mMDPC[U-99% 2H]1
0.4 mMsodium azide1
Sample conditionspH: 5 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Biospincollection
Sparky3.11Goddarddata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 361 / NOE intraresidue total count: 0 / NOE medium range total count: 104 / NOE sequential total count: 109 / Hydrogen bond constraints total count: 24
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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