BMRB Entry 34113
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34113
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Title: Structure of PsDef1 defensin from Pinus sylvestris PubMed: 28528214
Deposition date: 2017-03-03 Original release date: 2017-06-02
Authors: Khairutdinov, B.; Ermakova, E.; Bessolitsyna, E.; Toporkova, Y.; Tarasova, N.; Kovaleva, V.; Zuev, Y.; Nesmelova, I.
Citation: Khairutdinov, Bulat; Ermakova, Elena; Yusypovych, Yuri; Bessolicina, Elena; Tarasova, Nadezhda; Toporkova, Yana; Kovaleva, Valentina; Zuev, Yuriy; Nesmelova, Irina. "NMR structure, conformational dynamics, and biological activity of PsDef1 defensin from Pinus sylvestris." Biochim. Biophys. Acta 1865, 1085-1094 (2017).
Assembly members:
entity_1, polymer, 50 residues, 5611.574 Da.
Natural source: Common Name: Scots pine Taxonomy ID: 3349 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Pinus sylvestris
Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3)
Entity Sequences (FASTA):
entity_1: RMCKTPSGKFKGYCVNNTNC
KNVCRTEGFPTGSCDFHVAG
RKCYCYKPCP
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 200 |
| 15N chemical shifts | 51 |
| 1H chemical shifts | 322 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
Entities:
Entity 1, entity_1 50 residues - 5611.574 Da.
| 1 | ARG | MET | CYS | LYS | THR | PRO | SER | GLY | LYS | PHE | |
| 2 | LYS | GLY | TYR | CYS | VAL | ASN | ASN | THR | ASN | CYS | |
| 3 | LYS | ASN | VAL | CYS | ARG | THR | GLU | GLY | PHE | PRO | |
| 4 | THR | GLY | SER | CYS | ASP | PHE | HIS | VAL | ALA | GLY | |
| 5 | ARG | LYS | CYS | TYR | CYS | TYR | LYS | PRO | CYS | PRO |
Samples:
sample_1: PsDef1 0.4 mM; sodium acetate 10 mM
sample_2: PsDef1, [U-15N], 0.7 mM; sodium acetate 10 mM
sample_conditions_1: pH: 4.5; pressure: 1 atm; temperature: 306 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D DQF-COSY | sample_1 | anisotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | anisotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | anisotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | anisotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | anisotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | anisotropic | sample_conditions_1 |
| 2D 1H-13C HMBC | sample_1 | anisotropic | sample_conditions_1 |
| 2D 1H-13C TOCSY-HSQC | sample_1 | anisotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | anisotropic | sample_conditions_1 |
Software:
CNS, Brunger A. T. et.al. - refinement
NMR spectrometers:
- Bruker AvanceIII 700 MHz
- Bruker AvanceIII 600 MHz
- Bruker AvanceIII 500 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts