BMRB Entry 34720

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34720
MolProbity Validation Chart

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NMR-STAR v3 text file.
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Title:
Solution structure of thanatin-like derivative 4 in complex with E.coli LptA mutant Q62L
Deposition date:
2022-03-31
Original release date:
2023-05-30
Authors:
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, 118 residues, 12853.328 Da.
entity_2, polymer, 16 residues, 2007.387 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: VTGDTDQPIHIESDQQSLDM QGNVVTFTGNVIVTLGTIKI NADKVVVTRPGGEQGKEVID GYGKPATFYQMQDNGKPVEG HASQMHYELAKDFVVLTGNA YLQQVDSNIKGDKITYLV
entity_2: XXITYXNRXTXKCXRY

Data sets:
Data typeCount
13C chemical shifts467
15N chemical shifts117
1H chemical shifts866

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22

Entities:

Entity 1, unit_1 118 residues - 12853.328 Da.

1   VALTHRGLYASPTHRASPGLNPROILEHIS
2   ILEGLUSERASPGLNGLNSERLEUASPMET
3   GLNGLYASNVALVALTHRPHETHRGLYASN
4   VALILEVALTHRLEUGLYTHRILELYSILE
5   ASNALAASPLYSVALVALVALTHRARGPRO
6   GLYGLYGLUGLNGLYLYSGLUVALILEASP
7   GLYTYRGLYLYSPROALATHRPHETYRGLN
8   METGLNASPASNGLYLYSPROVALGLUGLY
9   HISALASERGLNMETHISTYRGLULEUALA
10   LYSASPPHEVALVALLEUTHRGLYASNALA
11   TYRLEUGLNGLNVALASPSERASNILELYS
12   GLYASPLYSILETHRTYRLEUVAL

Entity 2, unit_2 16 residues - 2007.387 Da.

1   EU0HYPILETHRTYRLE1ASNARGDABTHR
2   4FOLYSCYSDABARGTYR

Samples:

sample_1: Lipopolysaccharide export system protein LptA, [U-13C; U-15N], 300 ± 10 uM; sodium phosphate 20 mM; sodium chloride 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 HCCH-TOCSYsample_1isotropicsample_conditions_1

Software:

MOE v2019.01, Chemical Computing Group ULC. - refinement

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

CARA, Keller and Wuthrich - chemical shift assignment

CcpNmr Analysis v2.4, CCPN - peak picking

TopSpin v4.0, Bruker Biospin - processing

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