BMRB Entry 27086

Name: Heteronuclear chemical shifts of native cytotoxin-1 from N. oxiana
Published: 2017-09-15

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR27086

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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:

Heteronuclear chemical shifts of native cytotoxin-1 from N. oxiana

Deposition date:

2017-04-27

Original release date:

2017-09-15

Authors:

Dubinnyi, Maxim

Citation:

Citation: Dubovskii, Peter; Dubinnyi, Maxim; Konshina, Anastasia; Kazakova, Ekaterina; Sorokoumova, Galina; Ilyasova, Tatyana; Shulepko, Mikhail; Chertkova, Rita; Lyukmanova, Ekaterina; Dolgikh, Dmitry; Arseniev, Alexander; Efremov, Roman. "Structural and Dynamic "Portraits" of Recombinant and Native Cytotoxin I from Naja oxiana: How Close Are They?" Biochemistry 56, 4468-4477 (2017).
PubMed: 28749688

Assembly members:

Assembly members:
cytotoxin-1, polymer, 60 residues, 6813.2 Da.

Natural source:

Natural source: Common Name: Central Asian cobra Taxonomy ID: 8657 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Naja oxiana

Experimental source:

Experimental source: Production method: purified from the natural source Host organism: Naja oxiana

Entity Sequences (FASTA):

Entity Sequences (FASTA):
cytotoxin-1: LKCNKLVPIAYKTCPEGKNL CYKMFMMSDLTIPVKRGCID VCPKNSLLVKYVCCNTDRCN

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	222
15N chemical shifts	61
1H chemical shifts	434

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	cytotoxin-1, major form	1
2	cytotoxin-1, minor form	1

Entities:

Entity 1, cytotoxin-1, major form 60 residues - 6813.2 Da.

1	LEU	LYS	CYS	ASN	LYS	LEU	VAL	PRO	ILE	ALA
2	TYR	LYS	THR	CYS	PRO	GLU	GLY	LYS	ASN	LEU
3	CYS	TYR	LYS	MET	PHE	MET	MET	SER	ASP	LEU
4	THR	ILE	PRO	VAL	LYS	ARG	GLY	CYS	ILE	ASP
5	VAL	CYS	PRO	LYS	ASN	SER	LEU	LEU	VAL	LYS
6	TYR	VAL	CYS	CYS	ASN	THR	ASP	ARG	CYS	ASN

Samples:

sample_1: cytotoxin-1 3 ± 0.1 mM; H2O 0.5 ± 0.01 mL; D2O, [U-99% 2H], 0.1 ± 0.01 mL; potassium chloride 50 ± 1 mM

sample_2: cytotoxin-1 3 ± 0.1 mM; D2O, [U-100% 2H], 0.6 ± 0.01 mL; potassium chloride 50 ± 1 mM

sample_conditions_1: ionic strength: 50 mM; pH: 6.1; pressure: 1 bar; temperature: 303 K

sample_conditions_2: ionic strength: 50 mM; pD: 6.1; 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_2	isotropic	sample_conditions_2
2D DQF-COSY	sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_2
2D 1H-15N HSQC NH2 only	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_2

Software:

TOPSPIN, Bruker Biospin - chemical shift calculation, collection, data analysis

NMR spectrometers:

Bruker Avance 700 MHz

UNP	P01451
AlphaFold	P01451

1	LEU	LYS	CYS	ASN	LYS	LEU	VAL	PRO	ILE	ALA
2	TYR	LYS	THR	CYS	PRO	GLU	GLY	LYS	ASN	LEU
3	CYS	TYR	LYS	MET	PHE	MET	MET	SER	ASP	LEU
4	THR	ILE	PRO	VAL	LYS	ARG	GLY	CYS	ILE	ASP
5	VAL	CYS	PRO	LYS	ASN	SER	LEU	LEU	VAL	LYS
6	TYR	VAL	CYS	CYS	ASN	THR	ASP	ARG	CYS	ASN

1	LEU	LYS	CYS	ASN	LYS	LEU	VAL	PRO	ILE	ALA
2	TYR	LYS	THR	CYS	PRO	GLU	GLY	LYS	ASN	LEU
3	CYS	TYR	LYS	MET	PHE	MET	MET	SER	ASP	LEU
4	THR	ILE	PRO	VAL	LYS	ARG	GLY	CYS	ILE	ASP
5	VAL	CYS	PRO	LYS	ASN	SER	LEU	LEU	VAL	LYS
6	TYR	VAL	CYS	CYS	ASN	THR	ASP	ARG	CYS	ASN