BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 27572

Title: High-resolution NMR studies of antibiotics in cellular membranes   PubMed: 30262913

Deposition date: 2018-08-06 Original release date: 2018-08-09

Authors: Medeiros-Silva, Joao; Jekhmane, Shehrazade; Lucini Paioni, Alessandra; Gawarecka, Katarzyna; Baldus, Marc; Swiezewska, Ewa; Breukink, Eefjan; Weingarth, Markus

Citation: Medeiros-Silva, Joao; Jekhmane, Shehrazade; Lucini Paioni, Alessandra; Gawarecka, Katarzyna; Baldus, Marc; Swiezewska, Ewa; Breukink, Eefjan; Weingarth, Markus. "High-resolution NMR studies of antibiotics in cellular membranes"  Nat. Commun. 9, 3963-3963 (2018).

Assembly members:
Nisin_Z, polymer, 34 residues, Formula weight is not available
Lipid_II, polymer, 7 residues, Formula weight is not available

Natural source:   Common Name: Lactococcus lactis   Taxonomy ID: 1358   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Lactococcus lactis

Experimental source:   Production method: purified from the natural source   Host organism: Lactococcus lactis   Vector: n.a.

Entity Sequences (FASTA):
Nisin_Z: IXXIXLCXPGCKXGALMGCN MKXAXCNCSIHVXK
Lipid_II: XXAXKXX

Data sets:
Data typeCount
13C chemical shifts130
15N chemical shifts33
1H chemical shifts61

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1Nisin1
2Lipid II2

Entities:

Entity 1, Nisin 34 residues - Formula weight is not available

The X referes to Dehydrobutyrine, Dehydroalanine, D-AlalineS and AlanineS (Lanthionine) and Aminobutyric acid and AlanineS (3-Methyllanthionine). The CYS residues 7, 11, 19, 26, 28 should be regarded as an alanine crosslinked via a sulfour atom.

1   ILEDBUDALILEDHALEUCYSABUPROGLY
2   CYSLYSABUGLYALALEUMETGLYCYSASN
3   METLYSABUALAABUCYSASNCYSSERILE
4   HISVALDHALYS

Entity 2, Lipid II 7 residues - Formula weight is not available

1   NAGMUBALAFGALYSDALDAL

Samples:

sample_1: Nisin Z, [U-98% 13C; U-98% 15N], 150 nmol; Lipid II 75 nmol; DOPC 1875 nmol; TRIS 15 mM; sodium chloride 25 mM

sample_conditions_1: ionic strength: 65 mM; pH: 7.0; temperature: 290 K

Experiments:

NameSampleSample stateSample conditions
2D NHsample_1solidsample_conditions_1
2D CHsample_1solidsample_conditions_1
2D CCsample_1solidsample_conditions_1
3D HNCAsample_1solidsample_conditions_1
3D HNCOsample_1solidsample_conditions_1
3D HN(CO)CAsample_1solidsample_conditions_1

Software:

TOPSPIN v4.0.2, Bruker Biospin - collection, data analysis, processing

SPARKY v1.4, Goddard - chemical shift assignment, data analysis

NMR spectrometers:

  • Bruker Avance 950 MHz

Related Database Links:

UniProt P29559
Bactibase BAC049
PDB

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts