BMRB Entry 34393

Name: Bordetella pertussis adenylate cyclase toxin transmembrane segment 411-490 in DPC micelles
Published: 2020-05-08

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PDB ID: 6rfm
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34393
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:

Bordetella pertussis adenylate cyclase toxin transmembrane segment 411-490 in DPC micelles

Deposition date:

2019-04-15

Original release date:

2020-05-08

Authors:

Masin, J.; Bumba, L.; Veverka, V.

Citation:

Citation: Sukova, Anna; Bumba, Ladislav; Srb, Pavel; Veverka, Vaclav; Stanek, Ondrej; Holubova, Jana; Chmelik, Josef; Fiser, Radovan; Sebo, Peter; Masin, Jiri. "Negative charge of the AC-to-Hly linking segment modulates calcium-dependent membrane activities of Bordetella adenylate cyclase toxin" Biochim. Biophys. Acta Biomembr. 1862, 183310-183310 (2020).
PubMed: 32333856

Assembly members:

Assembly members:
entity_1, polymer, 80 residues, 8226.117 Da.

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSRSFSLGEVSDMAAVEAAE LEMTRQVLHAGARQDDAEPG VSGASAHWGQRALQGAQAVA AAQRLVHAIALMTQFGRAGS

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	303
15N chemical shifts	83
1H chemical shifts	499

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 80 residues - 8226.117 Da.

1	GLY	SER	ARG	SER	PHE	SER	LEU	GLY	GLU	VAL
2	SER	ASP	MET	ALA	ALA	VAL	GLU	ALA	ALA	GLU
3	LEU	GLU	MET	THR	ARG	GLN	VAL	LEU	HIS	ALA
4	GLY	ALA	ARG	GLN	ASP	ASP	ALA	GLU	PRO	GLY
5	VAL	SER	GLY	ALA	SER	ALA	HIS	TRP	GLY	GLN
6	ARG	ALA	LEU	GLN	GLY	ALA	GLN	ALA	VAL	ALA
7	ALA	ALA	GLN	ARG	LEU	VAL	HIS	ALA	ILE	ALA
8	LEU	MET	THR	GLN	PHE	GLY	ARG	ALA	GLY	SER

Samples:

sample_1: Cya411-490, [U-13C; U-15N], 450 uM; sodium phosphate 25 mM; sodium chloride 100 mM; TCEP 1 mM; DPC, [U-2H], 100 mM

sample_conditions_1: ionic strength: 125 mM; pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1

Software:

YASARA, YASARA - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

Sparky, Goddard - chemical shift assignment

TopSpin, Bruker Biospin - processing

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

1	GLY	SER	ARG	SER	PHE	SER	LEU	GLY	GLU	VAL
2	SER	ASP	MET	ALA	ALA	VAL	GLU	ALA	ALA	GLU
3	LEU	GLU	MET	THR	ARG	GLN	VAL	LEU	HIS	ALA
4	GLY	ALA	ARG	GLN	ASP	ASP	ALA	GLU	PRO	GLY
5	VAL	SER	GLY	ALA	SER	ALA	HIS	TRP	GLY	GLN
6	ARG	ALA	LEU	GLN	GLY	ALA	GLN	ALA	VAL	ALA
7	ALA	ALA	GLN	ARG	LEU	VAL	HIS	ALA	ILE	ALA
8	LEU	MET	THR	GLN	PHE	GLY	ARG	ALA	GLY	SER

1	GLY	SER	ARG	SER	PHE	SER	LEU	GLY	GLU	VAL
2	SER	ASP	MET	ALA	ALA	VAL	GLU	ALA	ALA	GLU
3	LEU	GLU	MET	THR	ARG	GLN	VAL	LEU	HIS	ALA
4	GLY	ALA	ARG	GLN	ASP	ASP	ALA	GLU	PRO	GLY
5	VAL	SER	GLY	ALA	SER	ALA	HIS	TRP	GLY	GLN
6	ARG	ALA	LEU	GLN	GLY	ALA	GLN	ALA	VAL	ALA
7	ALA	ALA	GLN	ARG	LEU	VAL	HIS	ALA	ILE	ALA
8	LEU	MET	THR	GLN	PHE	GLY	ARG	ALA	GLY	SER

1	GLY	SER	ARG	SER	PHE	SER	LEU	GLY	GLU	VAL
2	SER	ASP	MET	ALA	ALA	VAL	GLU	ALA	ALA	GLU
3	LEU	GLU	MET	THR	ARG	GLN	VAL	LEU	HIS	ALA
4	GLY	ALA	ARG	GLN	ASP	ASP	ALA	GLU	PRO	GLY
5	VAL	SER	GLY	ALA	SER	ALA	HIS	TRP	GLY	GLN
6	ARG	ALA	LEU	GLN	GLY	ALA	GLN	ALA	VAL	ALA
7	ALA	ALA	GLN	ARG	LEU	VAL	HIS	ALA	ILE	ALA
8	LEU	MET	THR	GLN	PHE	GLY	ARG	ALA	GLY	SER