BMRB Entry 36411
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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/BMR36411
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Title: Aptamer enhancing peroxidase activity of myoglobin PubMed: 34095949
Deposition date: 2021-02-19 Original release date: 2021-08-26
Authors: Tsukakoshi, K.; Matsugami, A.; Khunathai, K.; Kanazashi, M.; Yamagishi, Y.; Nakama, K.; Oshikawa, D.; Hayashi, F.; Kuno, H.; Ikebukuro, K.
Citation: Tsukakoshi, Kaori; Yamagishi, Yasuko; Kanazashi, Mana; Nakama, Kenta; Oshikawa, Daiki; Savory, Nasa; Matsugami, Akimasa; Hayashi, Fumiaki; Lee, Jinhee; Saito, Taiki; Sode, Koji; Khunathai, Kanjana; Kuno, Hitoshi; Ikebukuro, Kazunori. "G-quadruplex-forming aptamer enhances the peroxidase activity of myoglobin against luminol." Nucleic Acids Res. 49, 6069-6081 (2021).
Assembly members:
DNA (5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3'), polymer, 16 residues, 5131.298 Da.
Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: not available not available
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
DNA (5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3'): GGGTGGGTTGGGAGGG
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 67 |
| 1H chemical shifts | 153 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | unit_1 | 1 |
Entities:
Entity 1, unit_1 16 residues - 5131.298 Da.
| 1 | DG | DG | DG | DT | DG | DG | DG | DT | DT | DG | ||||
| 2 | DG | DG | DA | DG | DG | DG |
Samples:
sample_1: DNA (5'-D(*(GUA)P*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3') 1 mM; DSS 100 uM; Potassium phosphate buffer pH 6.5 10 mM; D2O, [U-2H], 100%
sample_2: DNA (5'-D(*(GUA)P*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3') 1 mM; DSS 100 uM; Potassium phosphate buffer pH 6.5 10 mM; H2O 95%; D2O, [U-2H], 5%
sample_conditions_1: ionic strength: 10 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY 500ms | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY 50ms | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY 120ms | sample_1 | isotropic | sample_conditions_1 |
| 2D DQF-COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY 50ms | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY 250ms | sample_2 | isotropic | sample_conditions_1 |
| 2D JR-HMBC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
Software:
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
Sparky v3.114, Goddard - peak picking
TopSpin v3.5, Bruker Biospin - processing
X-PLOR NIH v2.48, Schwieters, Kuszewski, Tjandra and Clore - structure calculation
NMR spectrometers:
- Bruker AVANCE III 700 MHz
- Bruker AVANCE III 800 MHz