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- PDB-6go0: PLANTARICIN S-B IN 100 MM DPC MICELLES. THIS IS THE BETA PART OF ... -

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Basic information

Entry
Database: PDB / ID: 6go0
TitlePLANTARICIN S-B IN 100 MM DPC MICELLES. THIS IS THE BETA PART OF THE BACTERIOCIN PLANTARICIN S
ComponentsPlantaricin S beta protein
KeywordsANTIMICROBIAL PROTEIN / ANTIMICROBIAL PROTEIN Bacteriocin menbrane interacting peptide
Function / homologyPlantaricin S beta 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 beta protein


Theoretical massNumber of molelcules
Total (without water)2,8771
Polymers2,8771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2860 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 beta protein


Mass: 2877.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lactobacillus plantarum (bacteria) / References: UniProt: O32830

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic11D proton
121isotropic12D DQF-COSY
131isotropic12D 1H-1H TOCSY
141isotropic12D 1H-1H NOESY
151isotropic12D 1H-13C HSQC
161isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: micelle
Contents: 1 mM Plantaricin S-b, 95 % H2O, 5 % [U-2H] D2O, 100 mM [U-2H] DPC, 0.2 mM DSS, 95% H2O/5% D2O
Label: no labeling / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPlantaricin S-bnatural abundance1
95 %H2Onatural abundance1
5 %D2O[U-2H]1
100 mMDPC[U-2H]1
0.2 mMDSSnatural abundance1
Sample conditionsDetails: Sample of PlS-b was purchased from GENSCRIPT at above 98% purity and used as is without further purification, or addition of salts/buffers.
Ionic strength: 0 Not defined / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
TALOSCornilescu, Delaglio and Baxdata analysis
CARAKeller and Wuthrichchemical shift assignment
SparkyGoddardpeak picking
TopSpin2.4Bruker Biospincollection
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics / Software ordinal: 6
Details: refined using distance and dihedral restraints in DMSO using the RECOORD script
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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