BMRB Entry 17791
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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/BMR17791
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Title: Structure of the duplex containing HNE derived (6S,8R,11S) gamma-HO-PdG when placed opposite dT
Deposition date: 2011-07-19 Original release date: 2012-08-30
Authors: Huang, Hai; Wang, Hao; Kozekova, Albena; LLoyd, R.; Rizzo, Carmelo; Stone, Michael
Citation: Huang, Hai; Wang, Hao; Kozekova, Albena; LLoyd, R.; Rizzo, Carmelo; Stone, Michael. "Ring-chain tautomerization of trans-4-hydroxynonenal derived (6S,8R,11S) gamma-hydroxy-1,N2-propano-deoxyguanosine adduct when placed opposite 2'-deoxythymidine in duplex" Not known ., .-..
Assembly members:
DNA_(5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3'), polymer, 12 residues, 3663.422 Da.
DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3'), polymer, 12 residues, 3678.433 Da.
HNE, non-polymer, 156.222 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(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3'): GCTAGCGAGTCC
DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3'): GGACTTGCTAGC
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 141 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA_(5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3') | 1 |
| 2 | DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3') | 2 |
| 3 | HNE | 3 |
Entities:
Entity 1, DNA_(5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3') 12 residues - 3663.422 Da.
| 1 | DG | DC | DT | DA | DG | DC | DG | DA | DG | DT | ||||
| 2 | DC | DC |
Entity 2, DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3') 12 residues - 3678.433 Da.
| 1 | DG | DG | DA | DC | DT | DT | DG | DC | DT | DA | ||||
| 2 | DG | DC |
Entity 3, HNE - C9 H16 O2 - 156.222 Da.
| 1 | HNE |
Samples:
sample_1: DNA_(5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3') 1 mM; DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3') 1 mM; HNE 1 mM; D2O 100%
sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | 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