BMRB Entry 30660

Name: Solution NMR structure of the nodule-specific cysteine-rich peptide NCR044 from Medicago truncatula
Published: 2019-10-04

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PDB ID: 6u6g
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30660
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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:

Solution NMR structure of the nodule-specific cysteine-rich peptide NCR044 from Medicago truncatula

Deposition date:

2019-08-29

Original release date:

2019-10-04

Authors:

Buchko, G.; Shah, D.

Citation:

Citation: Velivelli, Siva; Czymmek, Kirk; Li, Hui; Shaw, Jared; Buchko, Garry; Shah, Dilip. "Antifungal symbiotic peptide NCR044 exhibits unique structure and multifaceted mechanisms of action that confer plant protection" Proc. Natl. Acad. Sci. U.S.A. 117, 16043-16054 (2020).
PubMed: 32571919

Assembly members:

Assembly members:
entity_1, polymer, 36 residues, 4329.222 Da.

Natural source:

Natural source: Common Name: Barrel medic Taxonomy ID: 3880 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Medicago truncatula

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: AFIQLSKPCISDKECSIVKN YRARCRKGYCVRRRIR

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list

Data type	Count
13C chemical shifts	160
15N chemical shifts	36
1H chemical shifts	235

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 36 residues - 4329.222 Da.

1

ALA

PHE

ILE

GLN

LEU

SER

LYS

PRO

CYS

ILE

2

SER

ASP

LYS

GLU

CYS

SER

ILE

VAL

LYS

ASN

3

TYR

ARG

ALA

ARG

CYS

ARG

LYS

GLY

TYR

CYS

4

VAL

ARG

ILE

ARG

Samples:

sample_1: sodium chloride 50 ± 1 mM; sodium acetate 20 ± 1 mM; DEF19, [U-99% 13C; U-99% 15N], 1 ± 0.2 mM

sample_2: sodium chloride 50 ± 1 mM; sodium acetate 20 ± 1 mM; DEF19-2, [U-99% 13C; U-99% 15N], 1 ± 0.2 mM

sample_conditions_1: ionic strength: 70 mM; pH: 5.4; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	anisotropic	sample_conditions_1
3D HNCO	sample_1	anisotropic	sample_conditions_1
3D HNCACB	sample_1	anisotropic	sample_conditions_1
3D C(CO)NH	sample_1	anisotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	anisotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	anisotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	anisotropic	sample_conditions_1
Deuterium exchange	sample_1	anisotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	anisotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	anisotropic	sample_conditions_1
3D H(CCO)NH	sample_1	anisotropic	sample_conditions_1

Software:

Sparky v3.13, Goddard - data analysis

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure calculation

Felix v2007, Accelrys Software Inc. - processing

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

PSVS v1.5, Bhattacharya and Montelione - data analysis

NMR spectrometers:

Varian INOVA 600 MHz
Bruker AVANCE 750 MHz
Varian INOVA 750 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks