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- PDB-5l82: NMR Structure of Enterocin K1 in 50%/50% TFE/Water -

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Basic information

Entry
Database: PDB / ID: 5l82
TitleNMR Structure of Enterocin K1 in 50%/50% TFE/Water
ComponentsEnterococcin K1
KeywordsANTIBIOTIC / STRUCTURE FROM CYANA 2.1 / UNKNOWN FUNCTION / Membrane interacting / bacteriocin / EntK1
Function / homologyUncharacterized protein
Function and homology information
Biological speciesEnterococcus faecium EnGen0026 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsOvchinnikov, K. / Kristiansen, P.E. / Diep, D.
CitationJournal: Front Microbiol / Year: 2017
Title: The Leaderless Bacteriocin Enterocin K1 Is Highly Potent against Enterococcus faecium: A Study on Structure, Target Spectrum and Receptor.
Authors: Ovchinnikov, K.V. / Kristiansen, P.E. / Straume, D. / Jensen, M.S. / Aleksandrzak-Piekarczyk, T. / Nes, I.F. / Diep, D.B.
History
DepositionJun 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Experimental preparation
Category: atom_site / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_spectrometer
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_nmr_exptl_sample_conditions.temperature / _pdbx_nmr_exptl_sample_conditions.temperature_units / _pdbx_nmr_spectrometer.model
Revision 2.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enterococcin K1


Theoretical massNumber of molelcules
Total (without water)4,5721
Polymers4,5721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4050 Å2
MethodPISA
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 Enterococcin K1


Mass: 4572.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterococcus faecium EnGen0026 (bacteria) / References: UniProt: L2P7L3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic11H proton
121isotropic12D DQF-COSY
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-13C HSQC
151isotropic12D 1H-15N HSQC
161isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 1.0 mM Enterococcin K1, 50 % U-D TFE, 50 % H2O, 0.2 mM na DSS, trifluoroethanol/water
Label: nonlabeled EntK1 / Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMEnterococcin K1natural abundance1
50 %TFEU-D1
50 %H2Onatural abundance1
0.2 mMDSSna1
Sample conditionsIonic strength: 0 Not defined / Label: 1 / pH: 4 / Pressure: 1 atm / Temperature: 298.15 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 600 MHz / Details: Cryoprobe

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
SparkyGoddardpeak picking
XwinNMRBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: torsion angle dynamics / 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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