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- PDB-2jpm: Lactococcin G-b in TFE -

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Basic information

Entry
Database: PDB / ID: 2jpm
TitleLactococcin G-b in TFE
ComponentsBacteriocin lactococcin-G subunit beta
KeywordsANTIMICROBIAL PROTEIN / antimicrobial / membrane bound
Function / homologyBacteriocin, lactococcin-G / Lactococcin G-beta / killing of cells of another organism / defense response to bacterium / Bacteriocin lactococcin-G subunit beta
Function and homology information
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRogne, P. / Fimland, G. / Nissen-Meyer, J. / Kristiansen, P.E.
CitationJournal: Biochim.Biophys.Acta / Year: 2008
Title: Three-dimensional structure of the two peptides that constitute the two-peptide bacteriocin lactococcin G
Authors: Rogne, P. / Fimland, G. / Nissen-Meyer, J. / Kristiansen, P.E.
History
DepositionMay 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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
Revision 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriocin lactococcin-G subunit beta


Theoretical massNumber of molelcules
Total (without water)4,1181
Polymers4,1181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 102structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Bacteriocin lactococcin-G subunit beta


Mass: 4117.792 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Strain: LMGT 2081 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): RIL (DE3) pLysS / References: UniProt: P36962

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1413D 1H-15N TOCSY
1513D 1H-15N NOESY

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Sample preparation

DetailsContents: 1 mM [U-15N] Lactococcin Gb, 90 % [U-2H] TFE, 0.1 % TFA, 0.2 mM DSS, 90%TFE/10%H2O
Solvent system: 90%TFE/10%H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMLactococcin Gb[U-15N]1
90 %TFE[U-2H]1
0.1 %TFA1
0.2 mMDSS1
Sample conditionspH: 2.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARA1.4.1Keller and Wuthrichchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
MOLMOL2k.2Koradi, Billeter and Wuthrichvisualization
MOLMOL2k.2Koradi, Billeter and Wuthrichrmsd value calculation
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 530 / NOE intraresidue total count: 202 / NOE long range total count: 0 / NOE medium range total count: 140 / NOE sequential total count: 188 / Hydrogen bond constraints total count: 48 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 15 / Protein psi angle constraints total count: 15
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 102 / Conformers submitted total number: 20

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