BMRB Entry 34773
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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/BMR34773
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NMR-STAR v3 text file.
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Title: Solution Structure of thanatin-like derivative 5 in complex with E. coli LptA mutant Q62L PubMed: 37224246
Deposition date: 2022-11-26 Original release date: 2023-05-30
Authors: Oi, K.; Jurt, S.; Moehle, K.; Zerbe, O.
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).
Assembly members:
entity_1, polymer, 132 residues, 14521.276 Da.
entity_2, polymer, 16 residues, 1919.318 Da.
Natural source: Common Name: E. coli Taxonomy ID: 83333 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli
Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21
Entity Sequences (FASTA):
entity_1: VTGDTDQPIHIESDQQSLDM
QGNVVTFTGNVIVTLGTIKI
NADKVVVTRPGGEQGKEVID
GYGKPATFYQMQDNGKPVEG
HASQMHYELAKDFVVLTGNA
YLQQVDSNIKGDKITYLVKE
QKMQAFSDKGKR
entity_2: VXIIYXNRXTXKCXXY
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 576 |
| 15N chemical shifts | 147 |
| 1H chemical shifts | 1079 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | unit_1 | 1 |
| 2 | unit_2 | 2 |
Entities:
Entity 1, unit_1 132 residues - 14521.276 Da.
| 1 | VAL | THR | GLY | ASP | THR | ASP | GLN | PRO | ILE | HIS | ||||
| 2 | ILE | GLU | SER | ASP | GLN | GLN | SER | LEU | ASP | MET | ||||
| 3 | GLN | GLY | ASN | VAL | VAL | THR | PHE | THR | GLY | ASN | ||||
| 4 | VAL | ILE | VAL | THR | LEU | GLY | THR | ILE | LYS | ILE | ||||
| 5 | ASN | ALA | ASP | LYS | VAL | VAL | VAL | THR | ARG | PRO | ||||
| 6 | GLY | GLY | GLU | GLN | GLY | LYS | GLU | VAL | ILE | ASP | ||||
| 7 | GLY | TYR | GLY | LYS | PRO | ALA | THR | PHE | TYR | GLN | ||||
| 8 | MET | GLN | ASP | ASN | GLY | LYS | PRO | VAL | GLU | GLY | ||||
| 9 | HIS | ALA | SER | GLN | MET | HIS | TYR | GLU | LEU | ALA | ||||
| 10 | LYS | ASP | PHE | VAL | VAL | LEU | THR | GLY | ASN | ALA | ||||
| 11 | TYR | LEU | GLN | GLN | VAL | ASP | SER | ASN | ILE | LYS | ||||
| 12 | GLY | ASP | LYS | ILE | THR | TYR | LEU | VAL | LYS | GLU | ||||
| 13 | GLN | LYS | MET | GLN | ALA | PHE | SER | ASP | LYS | GLY | ||||
| 14 | LYS | ARG |
Entity 2, unit_2 16 residues - 1919.318 Da.
| 1 | VAL | HYP | ILE | ILE | TYR | LE1 | ASN | ARG | DAB | THR | ||||
| 2 | 4FO | LYS | CYS | DAB | DAB | TYR |
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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(COCA)CB | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D (HB)CB(CGCD)HD | sample_1 | isotropic | sample_conditions_1 |
| 2D (HB)CB(CGCDCE)HE | sample_1 | isotropic | sample_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 shifts
SPARKY: Backbone
or all simulated shifts