BMRB Entry 25672
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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/BMR25672
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Title: Base-displaced intercalated structure of the N-(2'deoxyguanosin-8-yl)-3-aminobenzanthrone DNA adduct PubMed: 26641105
Deposition date: 2015-06-23 Original release date: 2016-02-17
Authors: Politica, Dustin; Stone, Michael; Malik, Chanchal; Basu, Ashis
Citation: Politica, Dustin; Malik, Chanchal; Basu, Ashis; Stone, Michael. "Base-Displaced Intercalated Structure of the N-(2'-Deoxyguanosin-8-yl)-3-aminobenzanthrone DNA Adduct" Chem. Res. Toxicol. 28, 2253-2266 (2015).
Assembly members:
DNA_(5'-D(*GP*TP*GP*CP*(ABG)P*TP*GP*TP*TP*TP*GP*T)-3'), polymer, 12 residues, 3873.430 Da.
DNA_(5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3'), polymer, 12 residues, 3609.425 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(*GP*TP*GP*CP*(ABG)P*TP*GP*TP*TP*TP*GP*T)-3'): GTGCXTGTTTGT
DNA_(5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3'): ACAAACACGCAC
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 184 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA (5'-D(*GP*TP*GP*CP*(ABG)P*TP*GP*TP*TP*TP*GP*T)-3') | 1 |
| 2 | DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3') | 2 |
Entities:
Entity 1, DNA (5'-D(*GP*TP*GP*CP*(ABG)P*TP*GP*TP*TP*TP*GP*T)-3') 12 residues - 3873.430 Da.
| 1 | DG | DT | DG | DC | 4E9 | DT | DG | DT | DT | DT | ||||
| 2 | DG | DT |
Entity 2, DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3') 12 residues - 3609.425 Da.
| 1 | DA | DC | DA | DA | DA | DC | DA | DC | DG | DC | ||||
| 2 | DA | DC |
Samples:
sample_1: DNA (5'-D(*GP*TP*GP*CP*(ABG)P*TP*GP*TP*TP*TP*GP*T)-3') 352 uM; DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3') 352 uM; sodium phosphate 10 mM; sodium chloride 100 mM; EDTA 50 uM
sample_2: DNA (5'-D(*GP*TP*GP*CP*(ABG)P*TP*GP*TP*TP*TP*GP*T)-3') 521 uM; DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3') 521 uM; sodium phosphate 10 mM; sodium chloride 100 mM; EDTA 50 uM
sample_conditions_1: ionic strength: 110 mM; pH: 7; pressure: 1 atm; temperature: 298 K
sample_conditions_2: ionic strength: 110 mM; 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 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_2 |
| 2D 1H-1H COSY | sample_2 | isotropic | sample_conditions_2 |
Software:
AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement
SPARKY, Goddard - chemical shift assignment, data analysis
TOPSPIN, Bruker Biospin - data analysis, processing
MARDIGRAS, Borgias, B. A. & James, T. L. - Restraint calculation
CORMA, Borgias, B. A. & James, T. L. - Validation
NMR spectrometers:
- Bruker Avance 900 MHz