BMRB Entry 19862
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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/BMR19862
MolProbity Validation Chart
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NMR-STAR v3 text file.
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Citation: Li, Liang; Brown, Kyle; Ma, Ruidan; Stone, Michael. "DNA Sequence Modulates Geometrical Isomerism of the trans-8,9-Dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxy Aflatoxin B1 Adduct" Chem. Res. Toxicol. 28, 225-237 (2015).
PubMed: 25587868
Assembly members:
DNA_(5'-D(*CP*TP*AP*AP*(FAG)P*CP*TP*TP*CP*A)-3'), polymer, 10 residues, 3350.311 Da.
DNA_(5'-D(*TP*GP*AP*AP*GP*CP*TP*TP*AP*G)-3'), polymer, 10 residues, 3084.066 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(*CP*TP*AP*AP*(FAG)P*CP*TP*TP*CP*A)-3'): CTAAXCTTCA
DNA_(5'-D(*TP*GP*AP*AP*GP*CP*TP*TP*AP*G)-3'): TGAAGCTTAG
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 133 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA (5'-D(*CP*TP*AP*AP*(FAG)P*CP*TP*TP*CP*A)-3') | 1 |
| 2 | DNA (5'-D(*TP*GP*AP*AP*GP*CP*TP*TP*AP*G)-3') | 2 |
Entities:
Entity 1, DNA (5'-D(*CP*TP*AP*AP*(FAG)P*CP*TP*TP*CP*A)-3') 10 residues - 3350.311 Da.
| 1 | DC | DT | DA | DA | FAG | DC | DT | DT | DC | DA |
Entity 2, DNA (5'-D(*TP*GP*AP*AP*GP*CP*TP*TP*AP*G)-3') 10 residues - 3084.066 Da.
| 1 | DT | DG | DA | DA | DG | DC | DT | DT | DA | DG |
Samples:
AGC_FAPY_modified_duplex_major_isomer: DNA (5'-D(*CP*TP*AP*AP*(FAG)P*CP*TP*TP*CP*A)-3') 0.5 mM; DNA (5'-D(*TP*GP*AP*AP*GP*CP*TP*TP*AP*G)-3') 0.5 mM; Sodium Chloride 100 mM; Sodium Phosphate 10 mM; EDTA 50 uM
sample_condition_AGC_major_isomer: ionic strength: 0.1 M; pH: 7; pressure: 1 atm; temperature: 283 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H COSY | AGC_FAPY_modified_duplex_major_isomer | isotropic | sample_condition_AGC_major_isomer |
| 2D 1H-1H NOESY | AGC_FAPY_modified_duplex_major_isomer | isotropic | sample_condition_AGC_major_isomer |
Software:
AMBER v12, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement
TOPSPIN v3, Bruker Biospin - collection, processing
SPARKY v3.115, Goddard - chemical shift assignment, peak picking
NMR spectrometers:
- Bruker Avance 800 MHz
- Bruker Avance 900 MHz