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- PDB-5lfi: lactococcin A immunity protein -

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Basic information

Entry
Database: PDB / ID: 5lfi
Titlelactococcin A immunity protein
ComponentsLactococcin-A immunity protein
KeywordsIMMUNE SYSTEM / Four-helix bundle / immunity protein / bacteriocin receptor
Function / homologyLactococcin-A immunity protein-like / Bacteriocin immunity protein family / bacteriocin immunity / Lactococcin-A immunity protein
Function and homology information
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsPersson, C. / Fuochi, V. / Pedersen, A. / Karlsson, B.G. / Nissen-Meyer, J. / Kristiansen, P.E. / Oppegard, C.
CitationJournal: Biochemistry / Year: 2016
Title: Nuclear Magnetic Resonance Structure and Mutational Analysis of the Lactococcin A Immunity Protein.
Authors: Kristiansen, P.E. / Persson, C. / Fuochi, V. / Pedersen, A. / Karlsson, G.B. / Nissen-Meyer, J. / Oppegard, C.
History
DepositionJul 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 19, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactococcin-A immunity protein


Theoretical massNumber of molelcules
Total (without water)13,2731
Polymers13,2731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8620 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Lactococcin-A immunity protein


Mass: 13273.202 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Gene: lciA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3M7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCO
121isotropic13D HNCA
131isotropic13D HN(CA)CB
141isotropic13D HN(CO)CA
151isotropic13D HN(COCA)CB
161isotropic13D HN(CA)CO
171isotropic13D 1H-15N NOESY
181isotropic13D 1H-15N TOCSY
191isotropic13D (H)CCH-TOCSY
1101isotropic13D 1H-13C NOESY aliphatic
1111isotropic13D 1H-13C NOESY aromatic
1121isotropic12D 1H-15N HSQC
1131isotropic12D 1H-13C HSQC aliphatic
1141isotropic12D 1H-13C HSQC aromatic

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-100% 13C; U-100% 15N] lactococcin A immunity protein, 90% H2O/10% D2O
Label: 13C/15N / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: lactococcin A immunity protein / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.4 M / Label: Conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 16

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