BMRB Entry 19222

Name: NMR Studies of DNA Support the Role of Pre-Existing Minor Groove Variations in Nucleosome Indirect Readout
Published: 2013-06-06

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19222

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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 Studies of DNA Support the Role of Pre-Existing Minor Groove Variations in Nucleosome Indirect Readout

Deposition date:

2013-05-03

Original release date:

2013-06-06

Authors:

Xu, Xiaoqian; Ben Imeddourene, Akli; Zargarian, Loussine; Foloppe, Nicolas; Mauffret, Olivier; Hartmann, Brigitte

Citation:

Citation: Xu, Xiaoqian; Ben Imeddourene, Akli; Zargarian, Loussine; Foloppe, Nicolas; Mauffret, Olivier; Hartmann, Brigitte. "NMR Studies of DNA Support the Role of Pre-Existing Minor Groove Variations in Nucleosome Indirect Readout" Biochemistry 53, 5601-5612 (2014).
PubMed: 25102280

Assembly members:

Assembly members:
DNA_dodecamer_1-1, polymer, 12 residues, Formula weight is not available
DNA_dodecamer_1-2, polymer, 12 residues, Formula weight is not available
DNA_dodecamer_2-1, polymer, 12 residues, Formula weight is not available
DNA_dodecamer_2-2, polymer, 12 residues, Formula weight is not available
DNA_dodecamer_3-1, polymer, 12 residues, Formula weight is not available
DNA_dodecamer_3-2, polymer, 12 residues, Formula weight is not available
DNA_dodecamer_4-1, polymer, 12 residues, Formula weight is not available
DNA_dodecamer_4-2, polymer, 12 residues, Formula weight is not available

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_dodecamer_1-1: TCGTAGCAAGCT
DNA_dodecamer_1-2: AGCTTGCTACGA
DNA_dodecamer_2-1: GCTCTAGCACCG
DNA_dodecamer_2-2: CGGTGCTAGAGC
DNA_dodecamer_3-1: CCGCTTAAACGC
DNA_dodecamer_3-2: GCGTTTAAGCGG
DNA_dodecamer_4-1: CGCACGTACGCG
DNA_dodecamer_4-2: CGCGTACGTGCG

Data sets:

assigned_chemical_shifts
RDCs
- RDC_list_1

Data type	Count
31P chemical shifts	264

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA dodecamer 1-1	1
2	DNA dodecamer 1-2	2
3	DNA dodecamer 2-1	3
4	DNA dodecamer 2-2	4
5	DNA dodecamer 3-1	5
6	DNA dodecamer 3-2	6
7	DNA dodecamer 4-1	7
8	DNA dodecamer 4-2	8

Entities:

Entity 1, DNA dodecamer 1-1 12 residues - Formula weight is not available

1

DT

DC

DG

DT

DA

DG

DC

DA

DG

2

DC

DT

Entity 2, DNA dodecamer 1-2 12 residues - Formula weight is not available

1

DA

DG

DC

DT

DG

DC

DT

DA

DC

2

DG

DA

Entity 3, DNA dodecamer 2-1 12 residues - Formula weight is not available

1

DG

DC

DT

DC

DT

DA

DG

DC

DA

DC

2

DC

DG

Entity 4, DNA dodecamer 2-2 12 residues - Formula weight is not available

1

DC

DG

DT

DG

DC

DT

DA

DG

DA

2

DG

DC

Entity 5, DNA dodecamer 3-1 12 residues - Formula weight is not available

1

DC

DG

DC

DT

DA

DC

2

DG

DC

Entity 6, DNA dodecamer 3-2 12 residues - Formula weight is not available

1

DG

DC

DG

DT

DA

DG

DC

2

DG

Entity 7, DNA dodecamer 4-1 12 residues - Formula weight is not available

1

DC

DG

DC

DA

DC

DG

DT

DA

DC

DG

2

DC

DG

Entity 8, DNA dodecamer 4-2 12 residues - Formula weight is not available

1

DC

DG

DC

DG

DT

DA

DC

DG

DT

DG

2

DC

DG

Samples:

sample_1: DNA dodecamer 1-1 1.5 ± 0.05 mM; DNA dodecamer 1-2 1.5 ± 0.05 mM; DNA dodecamer 2-1 1.5 ± 0.05 mM; DNA dodecamer 2-2 1.5 ± 0.05 mM; DNA dodecamer 3-1 1.5 ± 0.05 mM; DNA dodecamer 3-2 1.5 ± 0.05 mM; DNA dodecamer 4-1 1.5 ± 0.05 mM; DNA dodecamer 4-2 1.5 ± 0.05 mM

sample_conditions_1: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 293 K

sample_conditions_2: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 303 K

sample_conditions_3: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 313 K

sample_conditions_4: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_4
2D 1H-13C TROSY	sample_1	anisotropic	sample_conditions_4
2D 1H-13C HSQC	sample_1	anisotropic	sample_conditions_4
2D 1H-31P Hetero - Correlation	sample_1	isotropic	sample_conditions_1

Software:

SPARKY, T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Francisco - chemical shift assignment

NMRPIPE v8.2, F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Bax: NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR. 6, 277-293 (1995). - processing

NMR spectrometers:

Bruker Avance 500 MHz