BMRB Entry 15027

Name: NMR Structure of the B-DNA Dodecamer CTCGGCGCCATC
Published: 2009-10-09

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15027

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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:

NMR Structure of the B-DNA Dodecamer CTCGGCGCCATC

Deposition date:

2006-11-13

Original release date:

2009-10-09

Authors:

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

Citation:

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).
PubMed: 16881637

Assembly members:

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:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

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:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	203

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	subunit 1	1
2	subunit 2	2

Entities:

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

1

DC

DT

DC

DG

DC

DG

DC

DA

2

DT

DC

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

1

DG

DA

DT

DG

DC

DG

DC

DG

2

DA

DG

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:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	isotropic	sample_conditions_1
Magnitude COSY	sample_1	isotropic	sample_conditions_1
E-COSY	sample_1	isotropic	sample_conditions_2
DQF-COSY	sample_1	isotropic	sample_conditions_2
P-COSY	sample_1	isotropic	sample_conditions_2
2D NOESY	sample_2	isotropic	sample_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