BMRB Entry 16223

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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/BMR16223
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Title:
Aflatoxin Formamidopyrimidine alpha anomer in single strand DNA
Deposition date:
2009-03-24
Original release date:
2009-11-23
Authors:
Brown, Kyle
Citation:

Citation: Brown, Kyle; Voehler, Markus; Magee, Shane; Harris, Constance; Harris, Thomas; Stone, Michael. "Structural perturbations induced by the alpha-anomer of the aflatoxin B(1) formamidopyrimidine adduct in duplex and single-strand DNA."  J. Am. Chem. Soc. 131, 16096-16107 (2009).
PubMed: 19831353

Assembly members:

Assembly members:
DNA_(5'-D(*DCP*DTP*(FAG)P*DA)-3'), polymer, 4 residues, 1537.133 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(*DCP*DTP*(FAG)P*DA)-3'): CTXA

Data sets:
Data typeCount
1H chemical shifts46

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*DCP*DTP*(FAG)P*DA)-3')1

Entities:

Entity 1, DNA (5'-D(*DCP*DTP*(FAG)P*DA)-3') 4 residues - 1537.133 Da.

1   DCDTFAGDA

Samples:

sample_1: DNA (5'-D(*DCP*DTP*(FAG)P*DA)-3') 0.4 mM; D2O 100%; Sodium Phosphate 20 mM; NaCl 0.1 M; NaN3 10 uM; Na2EDTA 50 uM

sample_2: DNA (5'-D(*DCP*DTP*(FAG)P*DA)-3') 0.4 mM; H2O 90%; D2O 10%; Sodium Phosphate 20 mM; NaCl 0.1 M; NaN3 10 uM; Na2EDTA 50 uM

sample_conditions_1: ionic strength: 0.1 M; pH: 8.7; pressure: 1 atm; temperature: 278 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_1

Software:

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

SPARKY, Goddard - chemical shift assignment, data analysis

TOPSPIN, Bruker Biospin - processing

MARDIGRAS, Borgias, B.A. & James, T.L. - restraint generation

CORMA, James T.L. - structure validation

CURVES, Lavery, R. and Sklenar, H - data analysis

NMR spectrometers:

  • Bruker Advance 500 MHz