BMRB Entry 19620
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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/BMR19620
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Title: Solution structure of DNA duplex containing N3T-ethylene-N1I interstrand cross-link PubMed: 24931822
Deposition date: 2013-11-18 Original release date: 2014-06-30
Authors: Denisov, Alexey; O'Flaherty, Derek; Noronha, Anne; Wilds, Christopher
Citation: O'Flaherty, Derek; Denisov, Alexey; Noronha, Anne; Wilds, Christopher. "NMR Structure of an Ethylene Interstrand Cross-Linked DNA which Mimics the Lesion Formed by 1,3-Bis(2-chloroethyl)-1-nitrosourea." ChemMedChem 9, 2099-2103 (2014).
Assembly members:
DNA_(5'-D(*CP*AP*GP*TP*TP*CP*CP*A)-3'), polymer, 8 residues, 2386.612 Da.
DNA_(5'-D(*TP*GP*GP*AP*IP*CP*TP*G)-3'), polymer, 8 residues, 2467.646 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*AP*GP*TP*TP*CP*CP*A)-3'): CAGTTCCA
DNA_(5'-D(*TP*GP*GP*AP*IP*CP*TP*G)-3'): TGGAXCTG
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 120 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA (5'-D(*CP*AP*GP*TP*TP*CP*CP*A)-3') | 1 |
| 2 | DNA (5'-D(*TP*GP*GP*AP*IP*CP*TP*G)-3') | 2 |
Entities:
Entity 1, DNA (5'-D(*CP*AP*GP*TP*TP*CP*CP*A)-3') 8 residues - 2386.612 Da.
| 1 | DC | DA | DG | DT | DT | DC | DC | DA |
Entity 2, DNA (5'-D(*TP*GP*GP*AP*IP*CP*TP*G)-3') 8 residues - 2467.646 Da.
| 1 | DT | DG | DG | DA | EDI | DC | DT | DG |
Samples:
sample_2: DNA (5'-D(*CP*AP*GP*TP*TP*CP*CP*A)-3') 0.5 mM; DNA (5'-D(*TP*GP*GP*AP*IP*CP*TP*G)-3') 0.5 mM; NaCl 100 mM; sodium phosphate 15 mM; D2O, [U-100% 2H], 10%; H2O 90%
sample_1: DNA (5'-D(*CP*AP*GP*TP*TP*CP*CP*A)-3') 0.5 mM; DNA (5'-D(*TP*GP*GP*AP*IP*CP*TP*G)-3') 0.5 mM; NaCl 100 mM; sodium phosphate 15 mM; D2O, [U-100% 2H], 100%
sample_conditions_1: ionic strength: 0.1 M; pH: 7.5; pressure: 1 atm; temperature: 298 K
sample_conditions_2: ionic strength: 0.1 M; pH: 7.5; pressure: 1 atm; temperature: 273 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D DQF-COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-31P HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_2 |
Software:
CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRView, Johnson, One Moon Scientific - data analysis
VNMRJ, Varian - collection
NMR spectrometers:
- Varian Unity Inova 500 MHz
- Varian VNMRS 500 MHz