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- PDB-2lgn: Lactococcin 972 -

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Basic information

Entry
Database: PDB / ID: 2lgn
TitleLactococcin 972
ComponentsLactococcin 972
KeywordsANTIMICROBIAL PROTEIN / bacteriocin
Function / homologyImmunoglobulin-like - #2850 / Bacteriocin, lactococcin 972 / Bacteriocin (Lactococcin_972) / Immunoglobulin-like / Sandwich / Mainly Beta / Lactococcin 972
Function and homology information
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsTurner, D.L. / Lamosa, P. / Martinez, B.
Citation
Journal: To be Published
Title: Structure and properties of lactococcin 972 from Lactococcus lactis
Authors: Turner, D.L. / Lamosa, P. / Martinez, B.
#1: Journal: Microbiology / Year: 1996
Title: Lactococcin 972 : a homodimeric lactococcal bacteriocin whose primary target is not the plasma membrane
Authors: Martinez, B. / Suarez, J.E. / Rodriguez, A.
History
DepositionJul 29, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactococcin 972


Theoretical massNumber of molelcules
Total (without water)7,3921
Polymers7,3921
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 / 250target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Lactococcin 972


Mass: 7391.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Strain: IPLA 972 / References: UniProt: O86283

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: lactococcin 972 (Lcn972) is a bacteriocin produced by Lactococcus lactis IPLA 972
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY

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Sample preparation

DetailsContents: 1.3 mM Lcn972, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.3 mM / Component: Lcn972-1
Sample conditionsIonic strength: 0.1 / pH: 6.8 / Pressure: ambient / Temperature: 277 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
TopSpin3Bruker Biospincollection
TopSpin3Bruker Biospinprocessing
DYANAINDYANA extendedGuntert, Braun and Wuthrichstructure solution
DYANAINDYANA extendedGuntert, Braun and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2778 / NOE intraresidue total count: 585 / NOE long range total count: 1275 / NOE medium range total count: 322 / NOE sequential total count: 596
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 250 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.36 Å / Maximum upper distance constraint violation: 0.28 Å
NMR ensemble rmsDistance rms dev: 0.02 Å

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