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- PDB-6gnz: Plantaricin S-a in 100 mM DPC micelles. This is the alpha part of... -

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Basic information

Entry
Database: PDB / ID: 6gnz
TitlePlantaricin S-a in 100 mM DPC micelles. This is the alpha part of the bacteriocin plantaricin S.
ComponentsPlantaricin S alpha protein
KeywordsANTIMICROBIAL PROTEIN / ANTIMICROBIAL PROTEIN Bacteriocin menbrane interacting peptide
Function / homologyBacteriocin-type signal sequence / killing of cells of another organism / defense response to bacterium / Plantaricin S alpha protein
Function and homology information
Biological speciesLactobacillus plantarum (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsEkblad, B. / Kristiansen, P.E.
CitationJournal: Sci Rep / Year: 2019
Title: NMR structures and mutational analysis of the two peptides constituting the bacteriocin plantaricin S.
Authors: Ekblad, B. / Kristiansen, P.E.
History
DepositionJun 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 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 1.3Jun 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: Plantaricin S alpha protein


Theoretical massNumber of molelcules
Total (without water)2,9261
Polymers2,9261
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2730 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Plantaricin S alpha protein


Mass: 2926.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lactobacillus plantarum (bacteria) / References: UniProt: O32831

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic11D proton
121anisotropic12D NOESY
131anisotropic12D DQF-COSY
141anisotropic12D TOCSY
151anisotropic12D 1H-13C HSQC
161anisotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: bicelle
Contents: 1 mM Plantaricin Sb, 0.2 mM DSS, 100 mM [U-100% 2H] DPC, 95%
Label: Sample_1 / Solvent system: 95%
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPlantaricin Sbnatural abundance1
0.2 mMDSSnatural abundance1
100 mMDPC[U-100% 2H]1
Sample conditionsDetails: Peptide purchased at 98% purity from genscript used as is. no buffers added to the DPC micelles
Ionic strength: 0 Not defined / Label: condition 1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 600 MHz / Details: with cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CARAKeller and Wuthrichchemical shift assignment
SparkyGoddardpeak picking
TopSpin2.4Bruker Biospincollection
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: NOE and dihedral angle restraints used in refinement in dmso using the script ReCOORD
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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