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- PDB-5ujr: NMR Solution Structure of the Two-component Bacteriocin CbnXY -

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Basic information

Entry
Database: PDB / ID: 5ujr
TitleNMR Solution Structure of the Two-component Bacteriocin CbnXY
ComponentsBacteriocin
KeywordsANTIMICROBIAL PROTEIN
Function / homologyBacteriocin-type signal sequence / Bacteriocin
Function and homology information
Biological speciesCarnobacterium maltaromaticum (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsAcedo, J.Z. / Towle, K.M. / Lohans, C.T. / McKay, R.T. / Miskolzie, M. / Doerksen, T. / Vederas, J.C. / Martin-Visscher, L.A.
CitationJournal: FEBS Lett. / Year: 2017
Title: Identification and three-dimensional structure of carnobacteriocin XY, a class IIb bacteriocin produced by Carnobacteria.
Authors: Acedo, J.Z. / Towle, K.M. / Lohans, C.T. / Miskolzie, M. / McKay, R.T. / Doerksen, T.A. / Vederas, J.C. / Martin-Visscher, L.A.
History
DepositionJan 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
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


Theoretical massNumber of molelcules
Total (without water)3,5901
Polymers3,5901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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 Bacteriocin


Mass: 3590.177 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carnobacterium maltaromaticum (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q46313

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-15N HSQC
141isotropic12D 1H-13C HSQC
151isotropic13D (H)CCH-TOCSY
161isotropic13D 1H-15N NOESY
171isotropic13D 1H-15N TOCSY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-99% 13C; U-99% 15N] CbnX, 50 % [U-99% 2H] trifluoroethanol, 50 % water, 0.01 % DSS, trifluoroethanol/water
Label: CbnX / Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCbnX[U-99% 13C; U-99% 15N]1
50 %trifluoroethanol[U-99% 2H]1
50 %waternone1
0.01 %DSSnone1
Sample conditionsIonic strength: 0 Not defined / Label: conditions_1 / pH: 6 / Pressure: 760 mmHg / Temperature: 300 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
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
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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