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
MolProbity Validation Chart

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Title:
Solution structure of DNA duplex containing N3T-ethylene-N1I interstrand cross-link
Deposition date:
2013-11-18
Original release date:
2014-06-30
Authors:
Denisov, Alexey; O'Flaherty, Derek; Noronha, Anne; Wilds, Christopher
Citation:

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).
PubMed: 24931822

Assembly members:

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:

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

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

Data sets:
Data typeCount
1H chemical shifts120

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*CP*AP*GP*TP*TP*CP*CP*A)-3')1
2DNA (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   DCDADGDTDTDCDCDA

Entity 2, DNA (5'-D(*TP*GP*GP*AP*IP*CP*TP*G)-3') 8 residues - 2467.646 Da.

1   DTDGDGDAEDIDCDTDG

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:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-31P HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_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