BMRB Entry 25959

Name: nigellin-1.1
Published: 2017-01-19

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PDB ID: 2nb2
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25959
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: nigellin-1.1

Deposition date: 2016-01-20 Original release date: 2017-01-19

Authors: Bozin, Timur; Bocharov, Eduard; Rogozhin, Eugene

Citation: Rogozhin, Eugene; Kozlov, Sergey; Andreev, Yaroslav; Ryazantsev, Dmitry; Grishin, Eugene; Bozin, Timur; Bocharov, Eduard. "A novel type of hairpin-like defense peptides from blackseed (Nigella sativa L.) contains three disulfide bridges" J. Biol. Chem. ., .-..

Assembly members:
nigellin-1.1, polymer, 38 residues, 4224.849 Da.

Natural source: Common Name: eudicots Taxonomy ID: 555479 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Nigella not available

Experimental source: Production method: purified from the natural source Host organism: Nigella sativa L.

Entity Sequences (FASTA):
nigellin-1.1: DRYQDCLSECNSRCTYIPDY AGMRACIGLCAPACLTSR

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	104
1H chemical shifts	243

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	nigellin-1.1	1

Entities:

Entity 1, nigellin-1.1 38 residues - 4224.849 Da.

1

ASP

ARG

TYR

GLN

ASP

CYS

LEU

SER

GLU

CYS

2

ASN

SER

ARG

CYS

THR

TYR

ILE

PRO

ASP

TYR

3

ALA

GLY

MET

ARG

ALA

CYS

ILE

GLY

LEU

CYS

4

ALA

PRO

ALA

CYS

LEU

THR

SER

ARG

Samples:

sample_H2O: nigellin-1.1 1 mM; sodium chloride 50 mM; H2O 90%; D2O 10%

sample_D2O: nigellin-1.1 1 mM; sodium chloride 50 mM; D2O 100%

sample_conditions_303: ionic strength: 0.05 M; pH: 3.5; pressure: 1 atm; temperature: 303 K

sample_conditions_310: ionic strength: 0.05 M; pH: 3.5; pressure: 1 atm; temperature: 310 K

sample_conditions_296: ionic strength: 0.05 M; pH: 3.5; pressure: 1 atm; temperature: 296 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC aliphatic	sample_H2O	isotropic	sample_conditions_303
2D 1H-1H TOCSY	sample_H2O	isotropic	sample_conditions_296
2D 1H-1H TOCSY	sample_H2O	isotropic	sample_conditions_303
2D 1H-1H TOCSY	sample_H2O	isotropic	sample_conditions_310
2D 1H-1H NOESY	sample_H2O	isotropic	sample_conditions_303
2D DQF-COSY	sample_D2O	isotropic	sample_conditions_303

Software:

CARA, Keller and Wuthrich - chemical shift assignment, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - refinement, stereospecific assignment, structure solution

Molmol, Koradi, Billeter and Wuthrich - 3D visualization, data analysis, processing

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis, processing

ACME, Delaglio, Zhengrong and Bax - coupling constant measurement

NMR spectrometers:

Varian Uniform NMR System 700 700 MHz