BMRB Entry 34626
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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/BMR34626
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Title: A self-complementary DNA dodecamer duplex contaning 5-hydroxymethylcitosine PubMed: 34748533
Deposition date: 2021-05-11 Original release date: 2021-10-30
Authors: Battistini, F.; Dans, P.; Terrazas, M.; Castellazzi, C.; Portella, G.; Labrador, M.; Villegas, N.; Brun-Heath, I.; Gonzalez, C.; Orozco, M.
Citation: Battistini, F.; Dans, P.; Terrazas, M.; Castellazzi, C.; Portella, G.; Labrador, M.; Villegas, N.; Brun-Heath, I.; Gonzalez, C.; Orozco, M.. "The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function" PLoS Comput. Biol. 17, e1009547-e1009547 (2021).
Assembly members:
entity_1, polymer, 8 residues, 2457.631 Da.
Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct
Experimental source: Production method: recombinant technology Host organism: synthetic construct
Entity Sequences (FASTA):
entity_1: CGAXGTCG
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 72 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | unit_1 | 1 |
| 2 | unit_2 | 1 |
Entities:
Entity 1, unit_1 8 residues - 2457.631 Da.
| 1 | DC | DG | DA | 5HC | DG | DT | DC | DG |
Samples:
sample_1: DNA (5'-D(*CP*GP*AP*(DH)P*GP*TP*CP*G)-3') 1 mM
sample_conditions_1: ionic strength: 125 mM; pH: 7.0; pressure: 1 atm; temperature: 278 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D DQF-COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
Software:
Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation
Sparky, Goddard - chemical shift assignment, peak picking
NMR spectrometers:
- Bruker AVANCE 600 MHz