BMRB Entry 34679
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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/BMR34679
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Title: 10bp DNA/DNA duplex PubMed: 36163470
Deposition date: 2021-11-16 Original release date: 2022-11-08
Authors: Qiang, L.; Marko, T.; Chaochao, F.; Jialiang, C.; Yifei, Z.; Kuan, L.; Hongjun, L.; Xuncheng, S.; Zhen, X.; Janez, P.; Chuanzheng, Z.
Citation: Li, Qiang; Trajkovski, Marko; Fan, Chaochao; Chen, Jialiang; Zhou, Yifei; Lu, Kuan; Li, Hongjun; Su, Xuncheng; Xi, Zhen; Plavec, Janez; Zhou, Chuanzheng. "4'-SCF3 -Labeling Constitutes a Sensitive 19 F NMR Probe for Characterization of Interactions in the Minor Groove of DNA" Angew. Chem. Int. Ed. Engl. 61, e202201848-e202201848 (2022).
Assembly members:
entity_1, polymer, 10 residues, 3003.992 Da.
entity_2, polymer, 10 residues, 3084.041 Da.
Natural source: Common Name: Octodon degus Taxonomy ID: 10160 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Octodon degus
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
entity_1: CCATTATAGC
entity_2: GCTATAATGG
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 188 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | unit_1 | 1 |
| 2 | unit_2 | 2 |
Entities:
Entity 1, unit_1 10 residues - 3003.992 Da.
| 1 | DC | DC | DA | DT | DT | DA | DT | DA | DG | DC |
Entity 2, unit_2 10 residues - 3084.041 Da.
| 1 | DG | DC | DT | DA | DT | DA | DA | DT | DG | DG |
Samples:
sample_1: DNA (5'-D(*CP*CP*AP*TP*TP*AP*TP*AP*GP*C)-3') 0.4 mM; DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3') 0.4 mM; sodium phosphate 10 mM
sample_2: DNA (5'-D(*CP*CP*AP*TP*TP*AP*TP*AP*GP*C)-3') 0.4 mM; DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3') 0.4 mM; sodium phosphate 10 mM
sample_conditions_1: ionic strength: 10 mM; pH: 7.0; pressure: 1 atm; temperature: 278 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D DQF-COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
Software:
TopSpin, Bruker Biospin - chemical shift assignment, collection
NMRFAM-SPARKY, Lee W, Tonelli M, Markley JL - chemical shift assignment, peak picking
Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation
NMR spectrometers:
- Bruker AVANCE NEO 600 MHz