BMRB Entry 17351

Name: Ribonucleotide Perturbation of DNA Structure: Solution Structure of [d(CGC)r(G)d(AATTCGCG)]2
Published: 2015-10-22

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PDB ID: 2l7d
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17351
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Ribonucleotide Perturbation of DNA Structure: Solution Structure of [d(CGC)r(G)d(AATTCGCG)]2 PubMed: 22390730

Deposition date: 2010-12-07 Original release date: 2015-10-22

Authors: DeRose, Eugene; Perera, Lalith; Michael, Murray; Thomas, Kunkel; Robert, London

Citation: DeRose, Eugene; Perera, Lalith; Murray, Michael; Kunkel, Thomas; London, Robert. "Solution Structure of the Dickerson DNA Dodecamer Containing a Single Ribonucleotide" Biochemistry 51, 2407-2416 (2012).

Assembly members:
rG4_substituted_Drew_Dickerson_dodecamer, polymer, 12 residues, 111.103 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):
rG4_substituted_Drew_Dickerson_dodecamer: CGCGAATTCGCG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	127
31P chemical shifts	11

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	rG4 substituted Drew Dickerson dodecamer, 1	1
2	rG4 substituted Drew Dickerson dodecamer, 2	1

Entities:

Entity 1, rG4 substituted Drew Dickerson dodecamer, 1 12 residues - 111.103 Da.

1

DC

DG

DC

G

DA

DT

DC

DG

2

DC

DG

Samples:

sample_1: rG4 substituted Drew Dickerson dodecamer 2.0 mM; sodium chloride 50.0 mM; sodium phosphate 50.0 mM; EDTA 0.5 mM

sample_2: rG4 substituted Drew Dickerson dodecamer 2.0 mM; sodium chloride 50.0 mM; sodium phosphate 50.0 mM; EDTA 0.5 mM; H2O 90%; D2O 10%

sample_3: rG4 substituted Drew Dickerson dodecamer 2.0 mM; sodium chloride 50.0 mM; sodium phosphate 50.0 mM; EDTA 0.5 mM; D2O 100%

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; 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-1H COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_2	anisotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-31P COSY	sample_1	isotropic	sample_conditions_1
2D 1H-31P J-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-31P HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-31P HSQC	sample_2	anisotropic	sample_conditions_1
2D CT-NOESY	sample_1	isotropic	sample_conditions_1
2D CT-NOESY	sample_2	anisotropic	sample_conditions_1

Software:

VNMRJ v2.1B, Varian - collection

NMRPipe v2010.190.16.149, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v8.0.b64, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

X-PLOR NIH v2.25, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 500 MHz