BMRB Entry 26004
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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/BMR26004
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Title: HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE SPIDER VENOM PEPTIDE U5-SCYTOTOXIN-STH1A PubMed: 27227898
Deposition date: 2016-03-18 Original release date: 2016-06-01
Authors: Loening, Nikolaus
Citation: Ariki, Nathanial; Munoz, Lisa; Armitage, Elizabeth; Goodstein, Francesca; George, Kathryn; Smith, Vanessa; Vetter, Irina; Herzig, Volker; King, Glenn; Loening, Nikolaus. "Characterization of Three Venom Peptides from the Spitting Spider Scytodes thoracica" PLoS One 11, e0156291-e0156291 (2016).
Assembly members:
U5-scytotoxin-Sth1a, polymer, 36 residues, 3912.2498 Da.
Natural source: Common Name: spitting spider Taxonomy ID: 1112478 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Scytodes thoracica
Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: PLIC-MBP
Entity Sequences (FASTA):
U5-scytotoxin-Sth1a: DETPDECVTRGNFCATPEVH
GDWCCGSLKCVSNSCR
- assigned_chemical_shifts
- spectral_peak_list
- peak_list_1
- peak_list_1_2
- peak_list_1_2_3
- peak_list_1_2_3_4
- peak_list_1_2_3_4_5
- peak_list_1_2_3_4_5_6
- peak_list_1_2_3_4_5_6_7
- peak_list_1_2_3_4_5_6_7_8
- peak_list_1_2_3_4_5_6_7_8_9
- peak_list_1_2_3_4_5_6_7_8_9_10
- peak_list_1_2_3_4_5_6_7_8_9_10_11
- peak_list_1_2_3_4_5_6_7_8_9_10_11_12
- peak_list_1_2_3_4_5_6_7_8_9_10_11_12_13
- peak_list_1_2_3_4_5_6_7_8_9_10_11_12_13_14
- peak_list_1_2_3_4_5_6_7_8_9_10_11_12_13_14_15
- peak_list_1_2_3_4_5_6_7_8_9_10_11_12_13_14_15_16
Data type | Count |
13C chemical shifts | 146 |
15N chemical shifts | 75 |
1H chemical shifts | 430 |
Additional metadata:
Assembly:
Entity Assembly ID | Entity Name | Entity ID |
---|---|---|
1 | SYTXE | 1 |
Entities:
Entity 1, SYTXE 36 residues - 3912.2498 Da.
1 | ASP | GLU | THR | PRO | ASP | GLU | CYS | VAL | THR | ARG | ||||
2 | GLY | ASN | PHE | CYS | ALA | THR | PRO | GLU | VAL | HIS | ||||
3 | GLY | ASP | TRP | CYS | CYS | GLY | SER | LEU | LYS | CYS | ||||
4 | VAL | SER | ASN | SER | CYS | ARG |
Samples:
sample_new_2: U5-scytotoxin-Sth1a, [U-13C; U-15N], 0.40 ± 0.10 mM
13C-15N: SYTXE, [U-98% 13C; U-98% 15N], 0.32 ± 0.0001 mM
15N: SYTXE, [U-98% 13C; U-98% 15N], 0.4 ± 0.0001 mM
sample_new_1: U5-scytotoxin-Sth1a, [U-13C; U-15N], 0.32 ± 0.10 mM
Standard: ionic strength: 0.030 M; pH: 6.500; pressure: 1.000 atm; temperature: 298.000 K
Experiments:
Name | Sample | Sample state | Sample conditions |
---|---|---|---|
3D HNCO | 13C-15N | isotropic | Standard |
HNCACO (H[N[ca[CO]]]) | 13C-15N | isotropic | Standard |
HNCOCACB (H[N[co[{CA|ca[C]}]]]) | 13C-15N | isotropic | Standard |
3D HNCACB | 13C-15N | isotropic | Standard |
2D 1H-13C HSQC/HMQC | 13C-15N | isotropic | Standard |
2D 1H-13C HSQC/HMQC | 13C-15N | isotropic | Standard |
2D 1H-13C HSQC/HMQC | 13C-15N | isotropic | Standard |
2D 1H-13C HSQC/HMQC | 13C-15N | isotropic | Standard |
2D 1H-15N HSQC/HMQC | 15N | isotropic | Standard |
2D 1H-15N HSQC/HMQC | 15N | isotropic | Standard |
2D 1H-1H TOCSY | 15N | isotropic | Standard |
2D 1H-1H NOESY | 15N | isotropic | Standard |
3D 1H-15N NOESY | 15N | isotropic | Standard |
3D 1H-15N TOCSY | 15N | isotropic | Standard |
2D 1H-15N HSQC/HMQC | 13C-15N | isotropic | Standard |
3D HCCH-TOCSY | 13C-15N | isotropic | Standard |
13C CT-HSQC | sample_new_1 | solution | Standard |
13C HSQC | sample_new_1 | solution | Standard |
13C AROMATIC HSQC | sample_new_1 | solution | Standard |
13C AROMATIC HSQC2 | sample_new_1 | solution | Standard |
15N HMQC (13C/15N SAMPLE) | sample_new_1 | solution | Standard |
HCCH TOCSY | sample_new_1 | solution | Standard |
HNCACB | sample_new_1 | solution | Standard |
HNCACO | sample_new_1 | solution | Standard |
HNCO | sample_new_1 | solution | Standard |
HNCOCACB | sample_new_1 | solution | Standard |
15N HMQC | sample_new_2 | solution | Standard |
15N HMQC2 | sample_new_2 | solution | Standard |
15N HSQC-NOESY | sample_new_2 | solution | Standard |
15N HSQC-TOCSY | sample_new_2 | solution | Standard |
1H NOESY | sample_new_2 | solution | Standard |
1H TOCSY | sample_new_2 | solution | Standard |
Software:
ARIA v2.3.2, Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E., Nilges M. - NOE assignment, structure calculation
AutoDep v4.3, PDBe - chemical shift assignment
CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - chemical shift assignment
CcpNmr_Analysis v2.4, CCPN - chemical shift assignment, project management
Talos-N v4.12, Yang Shen and Ad Bax - protein backbone dihedral angle prediction
NMR spectrometers:
- Bruker Avance III 600 MHz
- Bruker AVANCE 600 MHz
Related Database Links:
ArachnoServer | U5-scytotoxin-Sth1a |
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts