BMRB Entry 17788
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17788
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Title: Minor conformer of the DNA-peptide conjugate bridged by trimethylene tether PubMed: 21561113
Deposition date: 2011-07-18 Original release date: 2014-04-23
Authors: Huang, Hai; Kozekov, Ivan; Rizzo, Carmelo; McCullough, Amanda; LLoyd, R.; Stone, Michael
Citation: Huang, Hai; Wang, Hao; Voehler, Markus; Kozekova, Albena; Rizzo, Carmelo; McCullough, Amanda; Lloyd, R. Stephen; Stone, Michael. "-Hydroxy-1,N2-propano-2'-deoxyguanosine DNA adduct conjugates the N-terminal amine of the KWKK peptide via a carbinolamine linkage." Chem. Res. Toxicol. 24, 1123-1133 (2011).
Assembly members:
DNA_(5'-D(P*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3')_, polymer, 12 residues, 3045.029 Da.
DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3')_, polymer, 12 residues, 3045.029 Da.
entity_3, polymer, 5 residues, 591.773 Da.
Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
DNA_(5'-D(P*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3')_: GCTAGCGAGTCC
DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3')_: GGACTCGCTAGC
entity_3: XKWKK
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 177 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA_(5'-D(P*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3') | 1 |
| 2 | DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3') | 2 |
| 3 | entity_3 | 3 |
Entities:
Entity 1, DNA_(5'-D(P*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3') 12 residues - 3045.029 Da.
| 1 | DG | DC | DT | DA | DG | DC | DG | DA | DG | DT | ||||
| 2 | DC | DC |
Entity 2, DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3') 12 residues - 3045.029 Da.
| 1 | DG | DG | DA | DC | DT | DC | DG | DC | DT | DA | ||||
| 2 | DG | DC |
Entity 3, entity_3 5 residues - 591.773 Da.
| 1 | TME | LYS | TRP | LYS | LYS |
Samples:
sample_1: DNA_(5'-D(P*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3') 1 mM; DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3') 1 mM; entity_3 1 mM; D2O 100%
sample_conditions_1: ionic strength: 100 mM; pH: 8.9; pressure: 1 atm; temperature: 298 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:
AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement
NMR spectrometers:
- Bruker Avance 800 MHz