BMRB Entry 17351

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17351
MolProbity Validation Chart

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Title:
Ribonucleotide Perturbation of DNA Structure: Solution Structure of [d(CGC)r(G)d(AATTCGCG)]2
Deposition date:
2010-12-07
Original release date:
2015-10-22
Authors:
DeRose, Eugene; Perera, Lalith; Michael, Murray; Thomas, Kunkel; Robert, London
Citation:

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).
PubMed: 22390730

Assembly members:

Assembly members:
rG4_substituted_Drew_Dickerson_dodecamer, polymer, 12 residues, 111.103 Da.

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):
rG4_substituted_Drew_Dickerson_dodecamer: CGCGAATTCGCG

Data sets:
Data typeCount
1H chemical shifts127
31P chemical shifts11

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1rG4 substituted Drew Dickerson dodecamer, 11
2rG4 substituted Drew Dickerson dodecamer, 21

Entities:

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

1   DCDGDCGDADADTDTDCDG
2   DCDG

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:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_2anisotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-31P COSYsample_1isotropicsample_conditions_1
2D 1H-31P J-COSYsample_1isotropicsample_conditions_1
2D 1H-31P HSQCsample_1isotropicsample_conditions_1
2D 1H-31P HSQCsample_2anisotropicsample_conditions_1
2D CT-NOESYsample_1isotropicsample_conditions_1
2D CT-NOESYsample_2anisotropicsample_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