BMRB Entry 30720
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PDB ID:
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
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
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Title: Solution structure of antifungal plant defensin PvD1 PubMed: 32787086
Deposition date: 2020-02-03 Original release date: 2020-08-21
Authors: Harvey, P.
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).
Assembly members:
Knot1 domain-containing protein, polymer, 47 residues, 5459.170 Da.
Natural source: Common Name: Kidney bean Taxonomy ID: 3885 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Phaseolus vulgaris
Experimental source: Production method: .
Entity Sequences (FASTA):
Knot1 domain-containing protein: KTCENLADTYKGPCFTTGSC
DDHCKNKEHLRSGRCRDDFR
CWCTKNC
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 118 |
| 15N chemical shifts | 25 |
| 1H chemical shifts | 293 |
Additional metadata:
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 | THR | GLY | SER | CYS | ||||
| 3 | ASP | ASP | HIS | CYS | LYS | ASN | LYS | GLU | HIS | LEU | ||||
| 4 | ARG | SER | GLY | ARG | CYS | ARG | ASP | 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 shifts
SPARKY: Backbone
or all simulated shifts