BMRB Entry 25574

Name: Spatial Structure of Antimicrobial Peptide SmAMP2-2c from Seeds of Stellaria media
Published: 2016-06-27

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PDB ID: 2n1s
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25574
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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:

Spatial Structure of Antimicrobial Peptide SmAMP2-2c from Seeds of Stellaria media

Deposition date:

2015-04-16

Original release date:

2016-06-27

Authors:

Bozin, Timur; Bocharov, Eduard; Panova, Stanislava; Vassilevski, Alexander

Citation:

Citation: Vassilevski, Alexander; Bozin, Timur; Musolyamov, Alexander; Panova, Stanislava; Slavokhotova, Anna; Mitkevich, Vladimir; Finkina, Ekaterina; Nikonorova, Alexandra; Ovchinnikova, Tatyana; Arseniev, Alexander; Babakov, Alexei; Bocharov, Eduard; Grishin, Eugene; Egorov, Tsezi. "Common chickweed (Stellaria media) antifungal peptides with chitin-binding domain provide unique plant defense strategy." Molecular Plant ., .-..

Assembly members:

Assembly members:
SmAMP2-2c, polymer, 30 residues, 3002.410 Da.

Natural source:

Natural source: Common Name: Stellaria media Taxonomy ID: 13274 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Stellaria media

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-32b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SmAMP2-2c: AAGQCYRGRCSGGLCCSKYG YCGSGPAYCG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	81
1H chemical shifts	162

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	SmAMP2-2c	1

Entities:

Entity 1, SmAMP2-2c 30 residues - 3002.410 Da.

1	ALA	ALA	GLY	GLN	CYS	TYR	ARG	GLY	ARG	CYS
2	SER	GLY	GLY	LEU	CYS	CYS	SER	LYS	TYR	GLY
3	TYR	CYS	GLY	SER	GLY	PRO	ALA	TYR	CYS	GLY

Samples:

sample_inH2O: SmAMP2-2c 0.8 ± 0.1 mM; sodium acetate 20 ± 0.1 mM; sodium chloride 30 ± 0.1 mM

sample_inD2O: SmAMP2-2c 0.8 ± 0.1 mM; sodium acetate 20 ± 0.1 mM; sodium chloride 30 ± 0.1 mM

sample_4NOE: SmAMP2-2c 2 ± 0.1 mM; sodium acetate 10 ± 0.1 mM; sodium chloride 70 ± 0.1 mM

sample_conditions_30C: ionic strength: 0.08 M; pH: 4.5; pressure: 1 atm; temperature: 303 K

sample_conditions_10C: ionic strength: 0.05 M; pH: 4.5; pressure: 1 atm; temperature: 283 K

sample_conditions_40C: ionic strength: 0.05 M; pH: 4.5; pressure: 1 atm; temperature: 313 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D DQF-COSY	sample_inD2O	isotropic	sample_conditions_30C
2D 1H-13C HSQC	sample_inD2O	isotropic	sample_conditions_30C
2D 1H-1H NOESY	sample_4NOE	isotropic	sample_conditions_30C
2D 1H-1H TOCSY	sample_4NOE	isotropic	sample_conditions_40C
2D 1H-1H TOCSY	sample_inH2O	isotropic	sample_conditions_30C
2D 1H-1H TOCSY	sample_inH2O	isotropic	sample_conditions_10C

Software:

Molmol, Koradi, Billeter and Wuthrich - molecule viewer

CYANA v2.1, Guntert, Braun and Wuthrich - structure solution

ACME, Delaglio, Zhengrong and Bax - J-coupling measurement

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

CARA, Keller and Wuthrich - chemical shift assignment

NMR spectrometers:

Bruker DRX 600 MHz
Bruker DRX 700 MHz
Bruker DRX 800 MHz

1	ALA	ALA	GLY	GLN	CYS	TYR	ARG	GLY	ARG	CYS
2	SER	GLY	GLY	LEU	CYS	CYS	SER	LYS	TYR	GLY
3	TYR	CYS	GLY	SER	GLY	PRO	ALA	TYR	CYS	GLY

1	ALA	ALA	GLY	GLN	CYS	TYR	ARG	GLY	ARG	CYS
2	SER	GLY	GLY	LEU	CYS	CYS	SER	LYS	TYR	GLY
3	TYR	CYS	GLY	SER	GLY	PRO	ALA	TYR	CYS	GLY