BMRB Entry 19659

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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/BMR19659
MolProbity Validation Chart

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Title:
Structure of Exocyclic R,R N6,N6-(2,3-Dihydroxy-1,4-butadiyl)-2'-Deoxyadenosine Adduct Induced by 1,2,3,4-Diepoxybutane in DNA
Deposition date:
2013-12-05
Original release date:
2014-05-27
Authors:
Kowal, Ewa; Seneviratne, Uthpala; Wickramaratne, Susith; Doherty, Kathleen; Cao, Xiangkun; Tretyakova, Natalia; Stone, Michael
Citation:

Citation: Kowal, Ewa; Seneviratne, Uthpala; Wickramaratne, Susith; Doherty, Kathleen; Cao, Xiangkun; Tretyakova, Natalia; Stone, Michael. "Structures of Exocyclic R,R- and S,S-N(6),N(6)-(2,3-Dihydroxybutan-1,4-diyl)-2'-Deoxyadenosine Adducts Induced by 1,2,3,4-Diepoxybutane"  Chem. Res. Toxicol. 27, 805-817 (2014).
PubMed: 24741991

Assembly members:

Assembly members:
DNA_(5'-D(*CP*GP*GP*AP*CP*(RBD)P*AP*GP*AP*AP*G)-3'), polymer, 11 residues, 3103.081 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*(RBD)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 shifts201
homonuclear NOE values207

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1modified strand1
2complementary strand2

Entities:

Entity 1, modified strand 11 residues - 3103.081 Da.

1   DCDGDGDADCRBDDADGDADA
2   DG

Entity 2, complementary strand 11 residues - 3291.174 Da.

1   DCDTDTDCDTDTDGDTDCDC
2   DG

Samples:

sample_1: DNA (5'-D(*CP*GP*GP*AP*CP*(RBD)P*AP*GP*AP*AP*G)-3') 0.7 mM; DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3') 0.7 mM; sodium chloride 100 mM; EDTA 50 uM; sodium phosphate 10 mM; D2O 100%

sample_2: DNA (5'-D(*CP*GP*GP*AP*CP*(RBD)P*AP*GP*AP*AP*G)-3') 0.7 mM; DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3') 0.7 mM; sodium chloride 100 mM; EDTA 50 uM; sodium phosphate 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: 278 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D DQF-COSYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_2

Software:

CORMA, Brandan A. Borgias, Paul D. Thomas, He Liu, Anil Kumar - data analysis

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

MARDIGRAS, Brandan A. Borgias, Paul D. Thomas, He Liu, Anil Kumar, Marco Tonelli - conversion of intensities to distance restraints

SPARKY, Goddard - chemical shift assignment, chemical shift calculation, peak picking

TOPSPIN, Bruker Biospin - collection, processing

CURVES vplus web server, Christophe Blanchet, Marco Pasi, Krystyna Zakrzewska, Richard Lavery - data analysis

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 500 MHz