BMRB Entry 51630

Name: Clovibactin-Lipid II bound state
Published: 2023-06-23

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51630

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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: Clovibactin-Lipid II bound state PubMed: 37611581

Deposition date: 2022-09-16 Original release date: 2023-06-23

Authors: Weingarth, Markus; Shukla, Rhythm

Citation: Shukla, Rhythm; Peoples, Aaron; Ludwig, Kevin; Maity, Sourav; Derks, Maik; De Benedetti, Stefania; Krueger, Annika; Vermeulen, Bram; Harbig, Theresa; Lavore, Francesca; Kumar, Raj; Honorato, Rodrigo; Grein, Fabian; Nieselt, Kay; Liu, Yangping; Bonvin, Alexandre; Baldus, Marc; Kubitscheck, Ulrich; Breukink, Eefjan; Achorn, Catherine; Nitti, Anthony; Schwalen, Christopher; Spoering, Amy; Ling, Losee Lucy; Hughes, Dallas; Lelli, Moreno; Roos, Wouter; Lewis, Kim; Schneider, Tanja; Weingarth, Markus. "An antibiotic from an uncultured bacterium binds to an immutable target" Cell 186, 4059-4073 (2023).

Assembly members:
entity_1, polymer, 8 residues, Formula weight is not available
entity_2, polymer, 7 residues, Formula weight is not available

Natural source: Common Name: Eleftheria terrae Taxonomy ID: 1597781 Superkingdom: Bacteria Kingdom: not available Genus/species: Eleftheria terrae

Experimental source: Production method: purified from the natural source

Entity Sequences (FASTA):
entity_1: FXXSXALL
entity_2: AXKAAXX

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
13C chemical shifts	75
15N chemical shifts	10
1H chemical shifts	10

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

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

Entities:

Entity 1, Clovibactin 8 residues - Formula weight is not available

1

PHE

DLE

DLY

SER

HYN

ALA

LEU

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

1

ALA

DGL

LYS

ALA

MUB

NAG

Samples:

sample_1: Clovibactin, [U-100% 13C; U-100% 15N], 800 nM; Lipid II, [U-100% 13C; U-100% 15N], 400 nM

sample_conditions_1: ionic strength: 0.03 M; pH: 5.5; pressure: 1 atm; temperature: 260 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D CC	sample_1	isotropic	sample_conditions_1
2D NCA	sample_1	isotropic	sample_conditions_1
2D NCO	sample_1	isotropic	sample_conditions_1
2D NH	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN - chemical shift assignment, collection, processing

NMR spectrometers:

Bruker AVANCE III 1200 MHz
Bruker AVANCE III 800 MHz
Bruker AVANCE III 700 MHz

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