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
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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 PubMed: 24741991
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: 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).
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: 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*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
- assigned_chemical_shifts
- homonucl_NOEs
| Data type | Count |
| 1H chemical shifts | 201 |
| homonuclear NOE values | 207 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | modified strand | 1 |
| 2 | complementary strand | 2 |
Entities:
Entity 1, modified strand 11 residues - 3103.081 Da.
| 1 | DC | DG | DG | DA | DC | RBD | DA | DG | DA | DA | ||||
| 2 | DG |
Entity 2, complementary strand 11 residues - 3291.174 Da.
| 1 | DC | DT | DT | DC | DT | DT | DG | DT | DC | DC | ||||
| 2 | DG |
Samples:
sample_1: DNA (5, -D(*CP*GP*GP*AP*CP*(RBD)P*AP*GP*AP*AP*G)-3')', ; 2, DNA (5, ; 1, 3, ; 1, 4, ; 1, 5, ; 1, 6, ; 1
sample_2: DNA (5, -D(*CP*GP*GP*AP*CP*(RBD)P*AP*GP*AP*AP*G)-3')', ; 2, DNA (5, ; 2, 3, ; 2, 4, ; 2, 5, ; 2, 6, ; 2, 7, ; 2
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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 2D DQF-COSY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_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