BMRB Entry 27572

Name: High-resolution NMR studies of antibiotics in cellular membranes
Published: 2018-08-09

Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR27572

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

High-resolution NMR studies of antibiotics in cellular membranes

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:

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).
PubMed: 30262913

Assembly members:

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

Natural source:

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

Experimental source:

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

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	130
15N chemical shifts	33
1H chemical shifts	61

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Nisin	1
2	Lipid II	2

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

ILE

DBU

DAL

ILE

DHA

LEU

CYS

ABU

PRO

GLY

2

CYS

LYS

ABU

GLY

ALA

LEU

MET

GLY

CYS

ASN

3

MET

LYS

ABU

ALA

ABU

CYS

ASN

CYS

SER

ILE

4

HIS

VAL

DHA

LYS

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

1

NAG

MUB

ALA

FGA

LYS

DAL

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:

Name	Sample	Sample state	Sample conditions
2D NH	sample_1	solid	sample_conditions_1
2D CH	sample_1	solid	sample_conditions_1
2D CC	sample_1	solid	sample_conditions_1
3D HNCA	sample_1	solid	sample_conditions_1
3D HNCO	sample_1	solid	sample_conditions_1
3D HN(CO)CA	sample_1	solid	sample_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

UniProt	P29559
Bactibase	BAC049
PDB	1WCO 1WCO
AlphaFold	P29559