BMRB Entry 25863

Name: Adenylate cyclase toxin RTX domain from Bordetella pertussis
Published: 2016-06-15

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR25863

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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:

Adenylate cyclase toxin RTX domain from Bordetella pertussis

Deposition date:

2015-10-27

Original release date:

2016-06-15

Authors:

Veverka, Vaclav

Citation:

Citation: Bumba, Ladislav; Masin, Jiri; Macek, Pavel; Wald, Tomas; Motlova, Lucia; Bibova, Ilona; Klimova, Nela; Bednarova, Lucie; Veverka, Vaclav; Kachala, Michael; Svergun, Dmitri; Barinka, Cyril; Sebo, Peter. "Calcium-Driven Folding of RTX Domain beta-Rolls Ratchets Translocation of RTX Proteins through Type I Secretion Ducts" Mol. Cell. 62, 47-62 (2016).
PubMed: 27058787

Assembly members:

Assembly members:
RTX_domain, polymer, 153 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Bordetella pertussis Taxonomy ID: 520 Superkingdom: Bacteria Kingdom: not available Genus/species: Bordetella pertussis

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: n/a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RTX_domain: GSARDDVLIGDAGANVLNGL AGNDVLSGGAGDDVLLGDEG SDLLSGDAGNDDLFGGQGDD TYLFGVGYGHDTIYESGGGH DTIRINAGADQLWFARQGND LEIRILGTDDALTVHDWYRD ADHRVEIIHAANQAVDQAGI EKLVEAMAQYPDP

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_Ca+
- assigned_chem_shift_Ca-

Data type	Count
13C chemical shifts	717
15N chemical shifts	241
1H chemical shifts	241

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	ACT RTX domain	1

Entities:

Entity 1, ACT RTX domain 153 residues - Formula weight is not available

1

GLY

SER

ALA

ARG

ASP

VAL

LEU

ILE

GLY

2

ASP

ALA

GLY

ALA

ASN

VAL

LEU

ASN

GLY

LEU

3

ALA

GLY

ASN

ASP

VAL

LEU

SER

GLY

ALA

4

GLY

ASP

VAL

LEU

GLY

ASP

GLU

GLY

5

SER

ASP

LEU

SER

GLY

ASP

ALA

GLY

ASN

6

ASP

LEU

PHE

GLY

GLN

GLY

ASP

7

THR

TYR

LEU

PHE

GLY

VAL

GLY

TYR

GLY

HIS

8

ASP

THR

ILE

TYR

GLU

SER

GLY

HIS

9

ASP

THR

ILE

ARG

ILE

ASN

ALA

GLY

ALA

ASP

10

GLN

LEU

TRP

PHE

ALA

ARG

GLN

GLY

ASN

ASP

11

LEU

GLU

ILE

ARG

ILE

LEU

GLY

THR

ASP

12

ALA

LEU

THR

VAL

HIS

ASP

TRP

TYR

ARG

ASP

13

ALA

ASP

HIS

ARG

VAL

GLU

ILE

HIS

ALA

14

ALA

ASN

GLN

ALA

VAL

ASP

GLN

ALA

GLY

ILE

15

GLU

LYS

LEU

VAL

GLU

ALA

MET

ALA

GLN

TYR

16

PRO

ASP

PRO

Samples:

sample_Ca+: RTX_domain, [U-13C; U-15N], 0.5 mM; TRIS 5 mM; sodium chloride 50 mM; calcium chloride 10 mM; D2O, [U-2H], 5%; H2O 95%

sample_Ca-: RTX_domain, [U-13C; U-15N], 0.5 mM; TRIS 5 mM; sodium chloride 50 mM; D2O, [U-2H], 5%; H2O 95%

sample_conditions_1: ionic strength: 0.05 M; pH: 8; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_Ca+	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_Ca-	isotropic	sample_conditions_1
3D HNCACB	sample_Ca+	isotropic	sample_conditions_1
3D HNCACB	sample_Ca-	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_Ca+	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_Ca-	isotropic	sample_conditions_1
3D HNCO	sample_Ca+	isotropic	sample_conditions_1
3D HNCO	sample_Ca-	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

Bruker Avance 850 MHz
Bruker Avance 600 MHz

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