BMRB Entry 19917
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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/BMR19917
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Title: Solution NMR structure of DNA dodecamer containing the 5-hydroxycytosine
Deposition date: 2014-04-17 Original release date: 2014-09-08
Authors: Donahue, Patrick; Szulik, Marta; Stone, Michael
Citation: Szulik, Marta. "Characterization of 5-hydroxycytosine in DNA" Not known ., .-..
Assembly members:
DNA_(5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-3'), polymer, 12 residues, 3355.223 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
DNA_(5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-3'): CGCGAATTXGCG
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 70 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-3')_1 | 1 |
| 2 | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-3')_2 | 1 |
Entities:
Entity 1, DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-3')_1 12 residues - 3355.223 Da.
| 1 | DC | DG | DC | DG | DA | DA | DT | DT | 5OC | DG | ||||
| 2 | DC | DG |
Samples:
sample_1: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-3') 100 mM; D2O 10%; sodium phosphate 10 mM; sodium chloride 100 mM; sodium azide 11 mM; EDTA 0.05 mM; H2O 90%
sample_conditions_1: pH: 7; pressure: 1 atm; temperature: 288 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H COSY | sample_1 | isotropic | sample_conditions_1 |
Software:
SPARKY, Goddard - chemical shift assignment
AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement
TOPSPIN, Bruker Biospin - processing
NMR spectrometers:
- Bruker INOVA 900 MHz