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 17788

Title: Minor conformer of the DNA-peptide conjugate bridged by trimethylene tether   PubMed: 21561113

Authors: Huang, Hai; Kozekov, Ivan; Rizzo, Carmelo; McCullough, Amanda; LLoyd, R.; Stone, Michael

Citation: Huang, Hai; Wang, Hao; Voehler, Markus; Kozekova, Albena; Rizzo, Carmelo; McCullough, Amanda; Lloyd, R. Stephen; Stone, Michael. "-Hydroxy-1,N2-propano-2'-deoxyguanosine DNA adduct conjugates the N-terminal amine of the KWKK peptide via a carbinolamine linkage."  Chem. Res. Toxicol. 24, 1123-1133 (2011).

Assembly members:
DNA_(5'-D(P*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3')_, polymer, 12 residues, 3045.029 Da.
DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3')_, polymer, 12 residues, 3045.029 Da.
entity_3, polymer, 5 residues, 591.773 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(P*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3')_: GCTAGCGAGTCC
DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3')_: GGACTCGCTAGC
entity_3: XKWKK

Data sets:
Data typeCount
1H chemical shifts177

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1DNA_(5'-D(P*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3')1
2DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3')2
3entity_33

Entities:

Entity 1, DNA_(5'-D(P*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3') 12 residues - 3045.029 Da.

1   DGDCDTDADGDCDGDADGDT
2   DCDC

Entity 2, DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3') 12 residues - 3045.029 Da.

1   DGDGDADCDTDCDGDCDTDA
2   DGDC

Entity 3, entity_3 5 residues - 591.773 Da.

1   TMELYSTRPLYSLYS

Samples:

sample_1: DNA_(5'-D(P*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3') 1 mM; DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3') 1 mM; entity_3 1 mM; D2O 100%

sample_conditions_1: ionic strength: 100 mM; pH: 8.9; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1

Software:

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

NMR spectrometers:

  • Bruker Avance 800 MHz

Related Database Links: