BMRB Entry 34773

Title:
Solution Structure of thanatin-like derivative 5 in complex with E. coli LptA mutant Q62L
Deposition date:
2022-11-26
Original release date:
2023-05-30
Authors:
Oi, K.; Jurt, S.; Moehle, K.; Zerbe, O.
Citation:

Citation: Schuster, M.; Brabet, E.; Oi, K.; Desjonqueres, N.; Moehle, K.; Le Poupon, K.; Hell, S.; Gable, S.; Rithie, V.; Dillinger, S.; Zbinden, P.; Luther, A.; Li, C.; Stiegeler, S.; D'Arco, C.; Locher, H.; Remus, T.; DiMaio, S.; Motta, P.; Wach, A.; Jung, F.; Upert, G.; Obrecht, D.; Benghezal, M.; Zerbe, O.. "Peptidomimetic antibiotics disrupt the lipopolysaccharide transport bridge of drug-resistant Enterobacteriaceae."  Sci. Adv. 9, eadg3683-eadg3683 (2023).
PubMed: 37224246

Assembly members:

Assembly members:
entity_1, polymer, 132 residues, 14521.276 Da.
entity_2, polymer, 16 residues, 1919.318 Da.

Natural source:

Natural source:   Common Name: E. coli   Taxonomy ID: 83333   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21

Data sets:
Data typeCount
13C chemical shifts576
15N chemical shifts147
1H chemical shifts1079

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22

Entities:

Entity 1, unit_1 132 residues - 14521.276 Da.

1   VALTHRGLYASPTHRASPGLNPROILEHIS
2   ILEGLUSERASPGLNGLNSERLEUASPMET
3   GLNGLYASNVALVALTHRPHETHRGLYASN
4   VALILEVALTHRLEUGLYTHRILELYSILE
5   ASNALAASPLYSVALVALVALTHRARGPRO
6   GLYGLYGLUGLNGLYLYSGLUVALILEASP
7   GLYTYRGLYLYSPROALATHRPHETYRGLN
8   METGLNASPASNGLYLYSPROVALGLUGLY
9   HISALASERGLNMETHISTYRGLULEUALA
10   LYSASPPHEVALVALLEUTHRGLYASNALA
11   TYRLEUGLNGLNVALASPSERASNILELYS
12   GLYASPLYSILETHRTYRLEUVALLYSGLU
13   GLNLYSMETGLNALAPHESERASPLYSGLY
14   LYSARG

Entity 2, unit_2 16 residues - 1919.318 Da.

1   VALHYPILEILETYRLE1ASNARGDABTHR
2   4FOLYSCYSDABDABTYR

Samples:

sample_1: E. coli Lipopolysaccharide export system protein LptA mutant Q62L, [U-13C; U-15N], 300 ± 10 uM; Thanatin-like derivative 5, none, 500 ± 10 uM; sodium phosphate, none, 50 mM; sodium chloride, none, 150 mM

sample_conditions_1: ionic strength: 150 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(COCA)CBsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
2D (HB)CB(CGCD)HDsample_1isotropicsample_conditions_1
2D (HB)CB(CGCDCE)HEsample_1isotropicsample_conditions_1

Software:

CYANA v3.98, Guntert, Mumenthaler and Wuthrich - chemical shift assignment, structure calculation

MOE v2020.09, Chemical Computing Group ULC, 1010 Sherbook St. West, Suite #910, Montreal, QC, Canada, H3A 2R7, 2022 - refinement

CcpNmr Analysis v2.5.2, CCPN - peak picking

NMR spectrometers:

  • Bruker AVANCE NEO 700 MHz
  • Bruker AVANCE NEO 600 MHz

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