BMRB Entry 30720

Name: Solution structure of antifungal plant defensin PvD1
Published: 2020-08-21

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PDB ID: 6vpn
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30720
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:

Solution structure of antifungal plant defensin PvD1

Deposition date:

2020-02-03

Original release date:

2020-08-21

Authors:

Harvey, P.

Citation:

Citation: Skalska, Julia; Andrade, Vitor; Cena, Gabrielle; Harvey, Peta; Gaspar, Diana Maria Diez; Mello, Erica; Troeira Henriques, Sonia; Valle, Javier; Gomes, Valdirene; Conceicao, Katia; Castanho, Miguel; Andreu, David. "Synthesis, structure, and activity of the antifungal plant defensin PvD1" J. Med. Chem. 63, 9391-9402 (2020).
PubMed: 32787086

Assembly members:

Assembly members:
Knot1 domain-containing protein, polymer, 47 residues, 5459.170 Da.

Natural source:

Natural source: Common Name: Kidney bean Taxonomy ID: 3885 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Phaseolus vulgaris

Experimental source:

Experimental source: Production method: .

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Knot1 domain-containing protein: KTCENLADTYKGPCFTTGSC DDHCKNKEHLRSGRCRDDFR CWCTKNC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	118
15N chemical shifts	25
1H chemical shifts	293

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 47 residues - 5459.170 Da.

1

LYS

THR

CYS

GLU

ASN

LEU

ALA

ASP

THR

TYR

2

LYS

GLY

PRO

CYS

PHE

THR

GLY

SER

CYS

3

ASP

HIS

CYS

LYS

ASN

LYS

GLU

HIS

LEU

4

ARG

SER

GLY

ARG

CYS

ARG

ASP

PHE

ARG

5

CYS

TRP

CYS

THR

LYS

ASN

CYS

Samples:

sample_1: PvD1 1.0 mM

sample_2: PvD1 1.0 mM

sample_conditions_1: pH: 3.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-1H ECOSY	sample_2	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - processing

CcpNmr Analysis, CCPN - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

Bruker AVANCE III 600 MHz

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