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- PDB-2l96: Solution structure of LAK160-P7 -

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Basic information

Entry
Database: PDB / ID: 2l96
TitleSolution structure of LAK160-P7
ComponentsLAK160-P7
KeywordsDE NOVO PROTEIN / ANTIMICROBIAL PROTEIN / cationic / proline / ampiphatic
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsVermeer, L.S. / Bui, T.T. / Lan, Y. / Jumagulova, E. / Kozlowska, J. / McIntyre, C. / Drake, A.F. / Mason, J.A.
CitationJournal: To be Published
Title: The role of proline induced conformational flexibility in determining the antibacterial potency of linear cationic alpha-helical peptides
Authors: Vermeer, L.S. / Bui, T.T. / Lan, Y. / Jumagulova, E. / Kozlowska, J. / McIntyre, C. / Drake, A.F. / Mason, J.A.
History
DepositionFeb 1, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: LAK160-P7


Theoretical massNumber of molelcules
Total (without water)2,6671
Polymers2,6671
Non-polymers00
Water0
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 LAK160-P7


Mass: 2666.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized by solid phase synthesis / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Synthetic cationic anti-microbial peptide LAK160-P7
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 1mM LAK160-P7; 100mM SDS; 5mM TRIS; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMLAK160-P7-11
100 mMSDS-21
5 mMTRIS-31
Sample conditionsIonic strength: 105mM / pH: 7 / Pressure: ambient / Temperature: 310 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
Sparky3.113Goddardpeak picking
Sparky3.113Goddardchemical shift assignment
ARIA2.2Linge, O'Donoghue and Nilgesstructure solution
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
TopSpin3Bruker Biospincollection
TopSpin3Bruker Biospinprocessing
ProcheckNMR3.5.4Laskowski and MacArthurdata analysis
AQUA3.2Rullmann, Doreleijers and Kapteindata analysis
CNSSOLVE1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
Python2.6.5Python Software Foundationdata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: Standard ARIA refinement in water
NMR constraintsNOE constraints total: 82 / NOE intraresidue total count: 23 / NOE long range total count: 0 / NOE medium range total count: 24 / NOE sequential total count: 35
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 8

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