BMRB Entry 34773

Name: Solution Structure of thanatin-like derivative 5 in complex with E. coli LptA mutant Q62L
Published: 2023-05-30

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PDB ID: 8bss
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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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:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: VTGDTDQPIHIESDQQSLDM QGNVVTFTGNVIVTLGTIKI NADKVVVTRPGGEQGKEVID GYGKPATFYQMQDNGKPVEG HASQMHYELAKDFVVLTGNA YLQQVDSNIKGDKITYLVKE QKMQAFSDKGKR
entity_2: VXIIYXNRXTXKCXXY

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	576
15N chemical shifts	147
1H chemical shifts	1079

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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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

SER

LEU

ASP

MET

3

GLN

GLY

ASN

VAL

THR

PHE

THR

GLY

ASN

4

VAL

ILE

VAL

THR

LEU

GLY

THR

ILE

LYS

ILE

5

ASN

ALA

ASP

LYS

VAL

THR

ARG

PRO

6

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

LEU

THR

GLY

ASN

ALA

11

TYR

LEU

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

TYR

LE1

ASN

ARG

DAB

THR

2

4FO

LYS

CYS

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 peaks
SPARKY: Backbone or all simulated peaks