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- PDB-2ljt: C9L,C14L-LeuA -

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Basic information

Entry
Database: PDB / ID: 2ljt
TitleC9L,C14L-LeuA
ComponentsBacteriocin leucocin-A
KeywordsANTIMICROBIAL PROTEIN / Antimicrobial peptide
Function / homologyBacteriocin class IIa domain superfamily / Bacteriocin, class IIa / Bacteriocin, class IIa, conserved site / Class II bacteriocin / Bacteriocin class IIa family signature. / killing of cells of another organism / defense response to bacterium / extracellular region / Bacteriocin leucocin-A
Function and homology information
Biological speciesLeuconostoc gelidum (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsSit, C.S. / Lohans, C.T. / van Belkum, M.J. / Campbell, C.D. / Miskolzie, M. / Vederas, J.C.
CitationJournal: Chembiochem / Year: 2012
Title: Substitution of a Conserved Disulfide in the Type IIa Bacteriocin, Leucocin A, with L-Leucine and L-Serine Residues: Effects on Activity and Three-Dimensional Structure.
Authors: Sit, C.S. / Lohans, C.T. / van Belkum, M.J. / Campbell, C.D. / Miskolzie, M. / Vederas, J.C.
History
DepositionSep 23, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.3May 15, 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: Bacteriocin leucocin-A


Theoretical massNumber of molelcules
Total (without water)3,9571
Polymers3,9571
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 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Bacteriocin leucocin-A / Leucocin A-UAL 187 / Leu A


Mass: 3957.353 Da / Num. of mol.: 1 / Mutation: C9L, C14L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leuconostoc gelidum (bacteria) / Strain: UAL 187 / Gene: lcnA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P34034

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HSQC
1212D 1H-15N HSQC
1313D HNHA
1413D CBCA(CO)NH
1513D (H)CCH-TOCSY
1613D HNCO
1713D HN(CA)CB
1813D 1H-13C NOESY
1913D 1H-15N NOESY
11013D 1H-15N TOCSY

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Sample preparation

DetailsContents: 90 % [U-2H] TFE, 10 % H2O, 0.1 % TFA, 2.6 mM DSS, trifluoroethanol/water
Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
90 %TFE-1[U-2H]1
10 %H2O-21
0.1 %TFA-31
2.6 mMDSS-41
Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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