BMRB Entry 19853

Name: AFB1 FAPY modified AGA duplex
Published: 2019-08-09

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PDB ID: 2mmf
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19853
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

AFB1 FAPY modified AGA duplex

Deposition date:

2014-03-14

Original release date:

2019-08-09

Authors:

Li, Liang; Stone, Michael

Citation:

Citation: Li, Liang; Brown, Kyle; Ma, Ruidan; Stone, Michael. "DNA Sequence Modulates Geometrical Isomerism of the trans-8,9-Dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxy Aflatoxin B1 Adduct" Chem. Res. Toxicol. 28, 225-237 (2015).
PubMed: 25587868

Assembly members:

Assembly members:
DNA_(5'-D(*CP*TP*AP*AP*(FAG)P*AP*TP*TP*CP*A)-3'), polymer, 10 residues, 3374.335 Da.
DNA_(5'-D(*TP*GP*AP*AP*TP*CP*TP*TP*AP*G)-3'), polymer, 10 residues, 3059.053 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*TP*AP*AP*(FAG)P*AP*TP*TP*CP*A)-3'): CTAAXATTCA
DNA_(5'-D(*TP*GP*AP*AP*TP*CP*TP*TP*AP*G)-3'): TGAATCTTAG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	161

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (5'-D(CPTPAPAP(FAG)PAPTPTPCPA)-3')	1
2	DNA (5'-D(TPGPAPAPTPCPTPTPAPG)-3')	2

Entities:

Entity 1, DNA (5'-D(*CP*TP*AP*AP*(FAG)P*AP*TP*TP*CP*A)-3') 10 residues - 3374.335 Da.

1

DC

DT

DA

FAG

DA

DT

DC

DA

Entity 2, DNA (5'-D(*TP*GP*AP*AP*TP*CP*TP*TP*AP*G)-3') 10 residues - 3059.053 Da.

1

DT

DG

DA

DT

DC

DT

DA

DG

Samples:

AGA: DNA (5'-D(*CP*TP*AP*AP*(FAG)P*AP*TP*TP*CP*A)-3') 0.5 ± 0.2 mM; DNA (5'-D(*TP*GP*AP*AP*TP*CP*TP*TP*AP*G)-3') 0.5 ± 0.2 mM; Sodium Chloride 100 mM; Sodium Phosphate 10 mM; EDTA 50 uM

sample_condition_AGA: ionic strength: 0.1 M; pH: 7; pressure: 1 atm; temperature: 283 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H COSY	AGA	isotropic	sample_condition_AGA
2D 1H-1H NOESY	AGA	isotropic	sample_condition_AGA

Software:

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 900 MHz