BMRB Entry 34425

Name: NMR solution structure of Helicobacter pylori TonB-CTD (residues 179-285)
Published: 2020-03-23

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PDB ID: 6sly
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34425
MolProbity Validation Chart

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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:

NMR solution structure of Helicobacter pylori TonB-CTD (residues 179-285)

Deposition date:

2019-08-21

Original release date:

2020-03-23

Authors:

Ciragan, A.; Heikkinen, H.; Iwai, H.

Citation:

Citation: Ciragan, Annika; Backlund, Sofia; Mikula, Kornelia; Beyer, Hannes; Samuli Ollila, O.; Iwai, Hideo. "NMR Structure and Dynamics of TonB Investigated by Scar-Less Segmental Isotopic Labeling Using a Salt-Inducible Split Intein" Front. Chem. 8, 136-136 (2020).
PubMed: 32266203

Assembly members:

Assembly members:
entity_1, polymer, 107 residues, 11614.141 Da.

Natural source:

Natural source: Common Name: Helicobacter pylori Taxonomy ID: 210 Superkingdom: Bacteria Kingdom: not available Genus/species: Helicobacter pylori

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SEGATSEAQAYNPGVSNEFL MKIQTAISSKNRYPKMAQIR GIEGEVLVSFTINADGSVTD IKVVKSNTTDILNHAALEAI KSAAHLFPKPEETVHLKIPI AYSLKED

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1
- spectral_peak_list_2

Data type	Count
13C chemical shifts	453
15N chemical shifts	109
1H chemical shifts	743

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 107 residues - 11614.141 Da.

1

SER

GLU

GLY

ALA

THR

SER

GLU

ALA

GLN

ALA

2

TYR

ASN

PRO

GLY

VAL

SER

ASN

GLU

PHE

LEU

3

MET

LYS

ILE

GLN

THR

ALA

ILE

SER

LYS

4

ASN

ARG

TYR

PRO

LYS

MET

ALA

GLN

ILE

ARG

5

GLY

ILE

GLU

GLY

GLU

VAL

LEU

VAL

SER

PHE

6

THR

ILE

ASN

ALA

ASP

GLY

SER

VAL

THR

ASP

7

ILE

LYS

VAL

LYS

SER

ASN

THR

ASP

8

ILE

LEU

ASN

HIS

ALA

LEU

GLU

ALA

ILE

9

LYS

SER

ALA

HIS

LEU

PHE

PRO

LYS

PRO

10

GLU

THR

VAL

HIS

LEU

LYS

ILE

PRO

ILE

11

ALA

TYR

SER

LEU

LYS

GLU

ASP

Samples:

sample_1: TonB, [U-100% 13C; U-100% 15N], 0.5 mM

sample_conditions_1: ionic strength: 20 mM; pH: 6; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
3D H(CC)(CO)NH	sample_1	isotropic	sample_conditions_1
3D (H)CC(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1

Software:

CcpNMR v2.4.1, CCPN - chemical shift assignment

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure calculation

TALOS vN, Cornilescu, Delaglio and Bax - chemical shift assignment

Amber v14, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

PSVS v1.5, Bhattacharya and Montelione - data analysis

NMR spectrometers:

Bruker AVANCE 850 MHz

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