BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 15027

Title: NMR Structure of the B-DNA Dodecamer CTCGGCGCCATC   PubMed: 16881637

Authors: Wang, F.; DeMuro, N.; Elmquist, C.; Stover, J.; Rizzo, C.; Stone, M.

Citation: Wang, F.; DeMuro, N.; Elmquist, C.; Stover, J.; Rizzo, C.; Stone, M.. "Base-displaced intercalated structure of the food mutagen 2-amino-3-methylimidazo[4,5-f]quinoline in the recognition sequence of the NarI restriction enzyme, a hotspot for -2 bp deletions."  J. Am. Chem. Soc. 128, 10085-10095 (2006).

Assembly members:
5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3', polymer, 12 residues, Formula weight is not available
5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3', polymer, 12 residues, Formula weight is not available

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3': CTCGGCGCCATC
5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3': GATGGCGCCGAG

Data sets:
Data typeCount
1H chemical shifts203

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1subunit 11
2subunit 22

Entities:

Entity 1, subunit 1 12 residues - Formula weight is not available

1   DCDTDCDGDGDCDGDCDCDA
2   DTDC

Entity 2, subunit 2 12 residues - Formula weight is not available

1   DGDADTDGDGDCDGDCDCDG
2   DADG

Samples:

sample_1: 5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3' 0.7 mM; 5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3' 0.7 mM; potassium phosphate 10 mM; sodium chloride 100 mM; D2O 99.996%

sample_2: 5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3' 0.7 mM; 5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3' 0.7 mM; potassium phosphate 10 mM; sodium chloride 100 mM; D2O 10%

sample_conditions_1: ionic strength: 0.1 M; pH: 7.0; pressure: 1 atm; temperature: 288 K

sample_conditions_2: ionic strength: 0.1 M; pH: 7.0; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 0.1 M; pH: 7.0; pressure: 1 atm; temperature: 278 K

Experiments:

NameSampleSample stateSample conditions
2D NOESYsample_1isotropicsample_conditions_1
Magnitude COSYsample_1isotropicsample_conditions_1
E-COSYsample_1isotropicsample_conditions_2
DQF-COSYsample_1isotropicsample_conditions_2
P-COSYsample_1isotropicsample_conditions_2
2D NOESYsample_2isotropicsample_conditions_3

Software:

FELIX v95.0, Biosym/MSI - processing

CORMA v5.2, Keepers - iterative matrix relaxation

X-PLOR v3.1, Brunger - refinement

MARDIGRAS v5.2, Borgias - iterative matrix relaxation

NMR spectrometers:

  • Bruker CPTCI 800 MHz
  • Bruker TXI-Z, CP 600 MHz
  • Bruker TXI 500 MHz

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