BMRB Entry 30727

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR30727
MolProbity Validation Chart

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NMR-STAR v3 text file.
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Title:
NMR solution structure of natural scorpion toxin Cl13
Deposition date:
2020-02-24
Original release date:
2020-07-05
Authors:
del Rio Portilla, F.; Delepierre, M.; Lopez Giraldo, A.
Citation:

Citation: Lopez-Giraldo, A.; Olamendi-Portugal, T.; Riano-Umbarila, L.; Becerril, B.; Possani, L.; Delepierre, M.; Rio-Portilla, F.. "The three-dimensional structure of the toxic peptide Cl13 from the scorpion Centruroides limpidus."  Toxicon 184, 158-166 (2020).
PubMed: 32569846

Assembly members:

Assembly members:
entity_1, polymer, 67 residues, 7866.033 Da.

Natural source:

Natural source:   Common Name: Mexican scorpion   Taxonomy ID: 6876   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Centruroides limpidus

Experimental source:

Experimental source:   Production method: .

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: KEGYLVDYHTGCKYTCAKLG DNDYCVRECRLRYYQSAHGY CYAFACWCTHLYEQAVVWPL PNKRCKX

Data sets:
Data typeCount
13C chemical shifts241
15N chemical shifts65
1H chemical shifts459

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 67 residues - 7866.033 Da.

1   LYSGLUGLYTYRLEUVALASPTYRHISTHR
2   GLYCYSLYSTYRTHRCYSALALYSLEUGLY
3   ASPASNASPTYRCYSVALARGGLUCYSARG
4   LEUARGTYRTYRGLNSERALAHISGLYTYR
5   CYSTYRALAPHEALACYSTRPCYSTHRHIS
6   LEUTYRGLUGLNALAVALVALTRPPROLEU
7   PROASNLYSARGCYSLYSNH2

Samples:

sample_1: Cl13 2.5 mM

sample_conditions_1: ionic strength: 20 mM; pH: 4.7; pressure: 1 atm; temperature: 288 K

sample_conditions_2: ionic strength: 20 mM; pH: 4.7; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 20 mM; pH: 4.7; pressure: 1 atm; temperature: 303 K

sample_conditions_4: ionic strength: 20 mM; pH: 4.7; pressure: 1 atm; temperature: 313 K

sample_conditions_5: ionic strength: 20 mM; pH: 4.7; pressure: 1 atm; temperature: 318 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H TOCSYsample_1isotropicsample_conditions_2
2D 1H-1H NOESYsample_1isotropicsample_conditions_2
2D DQF-COSYsample_1isotropicsample_conditions_2
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_2
2D 1H-1H TOCSYsample_1isotropicsample_conditions_3
2D 1H-1H TOCSYsample_1isotropicsample_conditions_5
2D 1H-1H TOCSYsample_1isotropicsample_conditions_4
2D 1H-1H NOESYsample_1isotropicsample_conditions_5
2D 1H-1H NOESYsample_1isotropicsample_conditions_4
2D 1H-1H NOESYsample_1isotropicsample_conditions_3
2D 1H-1H NOESYsample_1isotropicsample_conditions_2
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_5
2D DQF-COSYsample_1isotropicsample_conditions_4
2D DQF-COSYsample_1isotropicsample_conditions_3
2D DQF-COSYsample_1isotropicsample_conditions_2
2D DQF-COSYsample_1isotropicsample_conditions_1
13C HMBCsample_1isotropicsample_conditions_2
13C HSQCTOCSYsample_1isotropicsample_conditions_2
2D 1H-13C HSQCsample_1isotropicsample_conditions_2
2D 1H-15N HSQCsample_1isotropicsample_conditions_2

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - geometry optimization, structure calculation

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

Amber v16, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - refinement

CARA v1.5, Keller and Wuthrich - chemical shift assignment

CARA, Keller and Wuthrich - peak picking

TALOS vN, Cornilescu, Delaglio and Bax - chemical shift calculation

NMR spectrometers:

  • Bruker AVANCE 800 MHz
  • 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