BMRB Entry 34261

Name: The solution structure of the LptA-Thanatin complex
Published: 2018-11-19

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PDB ID: 6gd5
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34261
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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:

The solution structure of the LptA-Thanatin complex

Deposition date:

2018-04-22

Original release date:

2018-11-19

Authors:

Moehle, K.; Zerbe, O.

Citation:

Citation: Vetterli, Stefan; Zerbe, Katja; Muller, Maik; Urfer, Matthias; Mondal, Milon; Wang, Shuang-Yan; Moehle, Kerstin; Zerbe, Oliver; Vitale, Alessandra; Pessi, Gabriella; Eberl, Leo; Wollscheid, Bernd; Robinson, John. "Thanatin Targets the Inter-Membrane Protein Bridge Required for Lipopolysaccharide Transport in Escherichia coli" Sci. Adv. 4, eaau2634-eaau2634 (2018).
PubMed: 30443594

Assembly members:

Assembly members:
entity_1, polymer, 117 residues, 12769.169 Da.
entity_2, polymer, 21 residues, 2441.984 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(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: VTGDTDQPIHIESDQQSLDM QGNVVTFTGNVIVTQGTIKI NADKVVVTRPGGEQGKEVID GYGKPATFYQMQDNGKPVEG HASQMHYELAKDFVVLTGNA YLQQVDSNIKGDKITYL
entity_2: GSKKPVPIIYCNRRTGKCQR M

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2
spectral_peak_list

Data type	Count
13C chemical shifts	502
15N chemical shifts	123
1H chemical shifts	826

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 117 residues - 12769.169 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

GLN

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

Entity 2, entity_2 21 residues - 2441.984 Da.

1

GLY

SER

LYS

PRO

VAL

PRO

ILE

TYR

2

CYS

ASN

ARG

THR

GLY

LYS

CYS

GLN

ARG

3

MET

Samples:

sample_1: entity_1 mM; entity_2 mM; sodium chloride 150 ± 2 mM; CHAPS 20 ± 1 mM; sodium phosphate 50 ± 2 mM

sample_2: entity_1 mM; entity_2 mM; sodium chloride 150 ± 2 mM; CHAPS 20 ± 1 mM; sodium phosphate 50 ± 2 mM

sample_3: entity_1 mM; entity_2 mM; sodium chloride 150 ± 2 mM; CHAPS 20 ± 1 mM; sodium phosphate 50 ± 2 mM

sample_4: entity_1 mM; entity_2 mM; sodium chloride 150 ± 2 mM; CHAPS 20 ± 1 mM; sodium phosphate 50 ± 2 mM

sample_conditions_1: ionic strength: 1.15 M; pH: 7.5; pressure: 1 bar; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_4	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_4	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
13C,15N filtered, 13C edited (aliph) NOESY	sample_4	isotropic	sample_conditions_1
3D HNCO	sample_4	isotropic	sample_conditions_1
13C,15N filtered, 13C edited (aliph.) NOESY	sample_2	isotropic	sample_conditions_1
3D 13C,15N-filtered, 15N edited NOESY	sample_4	isotropic	sample_conditions_1
3D 13C,15N-filtered, 15N edited NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_4	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_4	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_4	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_4	isotropic	sample_conditions_1
3D HNCACB	sample_4	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_4	isotropic	sample_conditions_1
HBCBCGCDHE	sample_2	isotropic	sample_conditions_1
HBCBCGCDCEHE	sample_2	isotropic	sample_conditions_1
13C,15N filtered, 13C edited (aro.) NOESY	sample_2	isotropic	sample_conditions_1
13C,15N filtered, 13C edited (arom.) NOESY	sample_4	isotropic	sample_conditions_1

Software:

CARA v1.48, Keller and Wuthrich - chemical shift assignment

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

XPLOR-NIH, Schwieters, Bruenger - refinement

CcpNMR, CCPN - peak picking

NMR spectrometers:

Bruker Avance-Neo 600 MHz
Bruker Avance-Neo 700 MHz

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