BMRB Entry 19912

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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/BMR19912
MolProbity Validation Chart

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Title:
MAJOR GROOVE ORIENTATION OF THE (2S)-N6-(2-HYDROXY-3-BUTEN-1-YL)-2'-DEOXYADENOSINE DNA ADDUCT INDUCED BY 1,2-EPOXY-3-BUTENE
Deposition date:
2014-04-16
Original release date:
2014-10-06
Authors:
Kowal, Ewa; Kotapati, Srikanth; Turo, Michael; Tretyakova, Natalia; Stone, Michael
Citation:

Citation: Kowal, Ewa; Kotapati, Srikanth; Turo, Michael; Tretyakova, Natalia; Stone, Michael. "Major Groove Orientation of the (2S)-N(6)-(2-Hydroxy-3-buten-1-yl)-2'-deoxyadenosine DNA Adduct Induced by 1,2-Epoxy-3-butene"  Chem. Res. Toxicol. ., .-..
PubMed: 25238403

Assembly members:

Assembly members:
DNA_(5'-D(*CP*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3'), polymer, 11 residues, 3084.065 Da.
DNA_(5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3'), polymer, 11 residues, 3291.174 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*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3'): CGGACXAGAAG
DNA_(5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3'): CTTCTTGTCCG

Data sets:
Data typeCount
1H chemical shifts163
homonuclear NOE values296

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*CP*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3')1
2DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3')2

Entities:

Entity 1, DNA (5'-D(*CP*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3') 11 residues - 3084.065 Da.

1   DCDGDGDADC6HBDADGDADA
2   DG

Entity 2, DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3') 11 residues - 3291.174 Da.

1   DCDTDTDCDTDTDGDTDCDC
2   DG

Samples:

sample_1: DNA (5'-D(*CP*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3') 0.51 mM; DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3') 0.51 mM; sodium chloride 100 mM; EDTA 50 uM; sodium phosphate (pH 7) 10 mM; D2O 100%

sample_2: DNA (5'-D(*CP*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3') 0.51 mM; DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3') 0.51 mM; sodium chloride 100 mM; EDTA 50 uM; sodium phosphate (pH 7) 10 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 288 K

sample_conditions_2: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 283 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure solution

CORMA, James, T. L. - data analysis

MARDIGRAS, Brandan A. Borgias, T. L. James - conversion of intensities to distance restraints

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 600 MHz