BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 30759

Title: Structure of a Stable Interstrand DNA Crosslink Involving an dA Amino Group and an Abasic Site   PubMed: 33382597

Deposition date: 2020-06-04 Original release date: 2021-05-03

Authors: Kellum Jr., A.; Qiu, D.; Voehler, M.; Martin, W.; Gates, K.; Stone, M.

Citation: Kellum Jr., A.; Qiu, D.; Voehler, M.; Martin, W.; Gates, K.; Stone, M.. "Structure of a Stable Interstrand DNA Cross-Link Involving a beta- N -Glycosyl Linkage Between an N 6 -dA Amino Group and an Abasic Site."  Biochemistry 60, 41-52 (2021).

Assembly members:
entity_1, polymer, 18 residues, 5480.576 Da.
entity_2, polymer, 18 residues, 5439.544 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: TATGTCTAAGTTCATCTA
entity_2: TAGATGAACXTAGACATA

Data sets:
Data typeCount
1H chemical shifts196

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22

Entities:

Entity 1, unit_1 18 residues - 5480.576 Da.

1   DTDADTDGDTDCDTDADADG
2   DTDTDCDADTDCDTDA

Entity 2, unit_2 18 residues - 5439.544 Da.

1   DTDADGDADTDGDADADCAAB
2   DTDADGDADCDADTDA

Samples:

sample_1: deoxyribonucleic acid 500 ± 0.2 uM

sample_2: deoxyribonucleic acid 500 ± 0.2 uM

sample_conditions_1: ionic strength: 120 mM; pH: 8; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 120 mM; pH: 8; pressure: 1 atm; temperature: 278 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1anisotropicsample_conditions_1
2D 1H-1H TOCSYsample_2anisotropicsample_conditions_1
2D 1H-1H NOESYsample_2anisotropicsample_conditions_2
2D 1H-1H COSYsample_1anisotropicsample_conditions_1

Software:

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - refinement, structure calculation

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

TopSpin, Bruker Biospin - data analysis, processing

NMR spectrometers:

  • Bruker AVANCE III 900 MHz