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- PDB-6gij: NMR structure of temporin B KKG6A in SDS micelles -

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Basic information

Entry
Database: PDB / ID: 6gij
TitleNMR structure of temporin B KKG6A in SDS micelles
ComponentstemporinB_KKG6A
KeywordsANTIMICROBIAL PROTEIN / AMP / temporin B analogue / structural modification
Function / homology
Function and homology information


other organism cell membrane / regulation of defense response to virus / defense response to fungus / killing of cells of another organism / defense response to Gram-positive bacterium / innate immune response / lipid binding / extracellular region / membrane
Similarity search - Function
Frog antimicrobial peptide, propeptide / Frog skin active peptide family signal and propeptide
Similarity search - Domain/homology
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing / distance geometry
AuthorsManzo, G. / Mason, J.A.
CitationJournal: Sci Rep / Year: 2019
Title: Minor sequence modifications in temporin B cause drastic changes in antibacterial potency and selectivity by fundamentally altering membrane activity.
Authors: Manzo, G. / Ferguson, P.M. / Gustilo, V.B. / Hind, C.K. / Clifford, M. / Bui, T.T. / Drake, A.F. / Atkinson, R.A. / Sutton, J.M. / Batoni, G. / Lorenz, C.D. / Phoenix, D.A. / Mason, A.J.
History
DepositionMay 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Category: pdbx_nmr_representative
Revision 1.2Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jun 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 1.5Jun 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

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Assembly

Deposited unit
A: temporinB_KKG6A


Theoretical massNumber of molelcules
Total (without water)1,6661
Polymers1,6661
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1880 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
Representative

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Components

#1: Protein/peptide temporinB_KKG6A


Mass: 1666.163 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The original peptide sequence is from Rana temporaria
Source: (synth.) synthetic construct (others) / References: UniProt: P79874*PLUS

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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: 100 mM U-98% 2H deuterated sodium dodecyl sulphate, 2 mM temporinB_KKG6A, 0.05 % w/w 2H 3-(trimethylsilyl)propionic-2,2,3,3-d4 acid, 90% H2O/10% D2O
Details: Peptide was solubilised in a a solution of SDS micelles at a L/P ratio of 50
Label: TBK_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 mMdeuterated sodium dodecyl sulphateU-98% 2H1
2 mMtemporinB_KKG6Anatural abundance1
0.05 % w/w3-(trimethylsilyl)propionic-2,2,3,3-d4 acid2H1
Sample conditionsIonic strength: no salts Not defined / Label: TBK_conditions / pH: 7 / 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
NameVersionDeveloperClassification
DYNAMODelaglio and Kuszewskirefinement
DYNAMODelaglio and Kuszewskistructure calculation
CARA1.9.1.2Keller and Wuthrichchemical shift assignment
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
Refinement
MethodSoftware ordinal
simulated annealing1
distance geometry2
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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