BMRB Entry 34039

Name: Minor form of the recombinant cytotoxin-1 from N. oxiana
Published: 2017-09-15

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PDB ID: 5lue
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34039
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: Minor form of the recombinant cytotoxin-1 from N. oxiana PubMed: 28749688

Deposition date: 2016-09-08 Original release date: 2017-09-15

Authors: Dubovskii, P.; Dubinnyi, M.; Shulepko, M.; Lyukmanova, E.; Dolgikh, D.; Kirpichnikov, M.; Efremov, R.

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).

Assembly members:
entity_1, polymer, 61 residues, 6962.535 Da.

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

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):
entity_1: MLKCNKLVPIAYKTCPEGKN LCYKMFMMSDLTIPVKRGCI DVCPKNSLLVKYVCCNTDRC N

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	277
15N chemical shifts	61
1H chemical shifts	454

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 61 residues - 6962.535 Da.

1

MET

LEU

LYS

CYS

ASN

LYS

LEU

VAL

PRO

ILE

2

ALA

TYR

LYS

THR

CYS

PRO

GLU

GLY

LYS

ASN

3

LEU

CYS

TYR

LYS

MET

PHE

MET

SER

ASP

4

LEU

THR

ILE

PRO

VAL

LYS

ARG

GLY

CYS

ILE

5

ASP

VAL

CYS

PRO

LYS

ASN

SER

LEU

VAL

6

LYS

TYR

VAL

CYS

ASN

THR

ASP

ARG

CYS

7

ASN

Samples:

sample_1: D2O, [U-99.9% 2H], 5 ± 0.1 v/v; H2O 95 ± 0.1 v/v; HCl 1 ± 0.1 uM; NaOH 3 ± 0.1 uM; recombinant cytotoxin-1, [U-99% 13C; U-99% 15N], 1 ± 0.1 mM

sample_conditions_1: pH: 6.5; pressure: 101325 Pa; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(COCA)CB	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
1D watergate	sample_1	isotropic	sample_conditions_1

Software:

CARA v1.8.4, Keller and Wuthrich - chemical shift assignment

CYANA v1.0.6, Guntert, Mumenthaler and Wuthrich - structure calculation

Rosetta v3.3, David Baker - refinement

TOPSPIN v2.0.a, Bruker Biospin - collection

NMR spectrometers:

Bruker Avance 700 MHz
Bruker Avance 600 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts