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- PDB-6gs5: NMR structure of temporin L in SDS micelles -

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Basic information

Entry
Database: PDB / ID: 6gs5
TitleNMR structure of temporin L in SDS micelles
ComponentsTemporin-L
KeywordsANTIMICROBIAL PROTEIN / AMP / temporin L / SDS micelle
Function / homologyother organism cell membrane / killing of cells of another organism / defense response to bacterium / innate immune response / lipid binding / extracellular region / membrane / Temporin-1Tl
Function and homology information
Biological speciesRana temporaria (common frog)
MethodSOLUTION NMR / distance geometry / simulated annealing
AuthorsManzo, G. / Mason, J.A.
CitationJournal: Sci Rep / Year: 2019
Title: Temporin L and aurein 2.5 have identical conformations but subtly distinct membrane and antibacterial activities.
Authors: Manzo, G. / Ferguson, P.M. / Hind, C.K. / Clifford, M. / Gustilo, V.B. / Ali, H. / Bansal, S.S. / Bui, T.T. / Drake, A.F. / Atkinson, R.A. / Sutton, J.M. / Lorenz, C.D. / Phoenix, D.A. / Mason, A.J.
History
DepositionJun 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Aug 14, 2019Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_representative
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_representative.conformer_id
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Temporin-L


Theoretical massNumber of molelcules
Total (without water)1,6431
Polymers1,6431
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1670 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1none

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Components

#1: Protein/peptide Temporin-L


Mass: 1642.983 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: TemporinL is an antimicrobial peptide found in Rana temporaria.
Source: (synth.) Rana temporaria (common frog) / References: UniProt: P57104

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: micelle
Contents: 2 mM Temporin L, 100 mM [U-2H] deuterated sodium dodecyl sulphate, 0.05 % w/w 2H 3-(trimethylsilyl)propionic-2,2,3,3-d4 acid, 90% H2O/10% D2O
Details: Peptide solubilised in a solution of SDS micelles at a L/P ratio of 50
Label: TL-SDS / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMTemporin Lnatural abundance1
100 mMdeuterated sodium dodecyl sulphate[U-2H]1
0.05 % w/w3-(trimethylsilyl)propionic-2,2,3,3-d4 acid2H1
Sample conditionsIonic strength: no salts Not defined / Label: TL-SDS_conditions / pH: 7.0 / Pressure: 1 atm / Temperature: 298 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
NameDeveloperClassification
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
X-PLORBrungerstructure calculation
X-PLORBrungerrefinement
Refinement
MethodSoftware ordinal
distance geometry4
simulated annealing3
NMR representativeSelection criteria: none
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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