BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 30052

Title: NMR solution structure of [Rp, Rp]-PT dsDNA   PubMed: 27169778

Authors: Lan, Wenxian; Hu, Zhongpei; Cao, Chunyang

Citation: Lan, Wenxian; Hu, Zhongpei; Cao, Chunyang. "Structural investigation into physiological DNA phosphorothioate modification"  Sci. Rep. 6, 25737-25737 (2016).

Assembly members:
DNA (5'-D(*CP*GP*(RSG)P*CP*CP*GP*CP*CP*GP*A)-3'), polymer, 10 residues, 3047.047 Da.
DNA (5'-D(*TP*CP*GP*GP*CP*GP*(RSG)P*CP*CP*G)-3'), polymer, 10 residues, 3078.058 Da.

Natural source:   Common Name: high GC Gram+   Taxonomy ID: 1916   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Streptomyces lividans

Experimental source:   Production method: recombinant technology   Host organism: Streptomyces lividans

Entity Sequences (FASTA):
DNA (5'-D(*CP*GP*(RSG)P*CP*CP*GP*CP*CP*GP*A)-3'): CGXCCGCCGA
DNA (5'-D(*TP*CP*GP*GP*CP*GP*(RSG)P*CP*CP*G)-3'): TCGGCGXCCG

Data sets:
Data typeCount
1H chemical shifts144
31P chemical shifts18

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 10 residues - 3047.047 Da.

1   DCDGGSDCDCDGDCDCDGDA

Entity 2, entity_2 10 residues - 3078.058 Da.

1   DTDCDGDGDCDGGSDCDCDG

Samples:

sample_1: [Rp, Rp]-PT dsDNA 1.0 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 360 mM; pH: 7.0; pressure: 1.0 atm; temperature: 298 K

sample_conditions_2: ionic strength: 360 mM; pH: 7.0; pressure: 1.0 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D NOESYsample_1anisotropicsample_conditions_1
2D TOCSYsample_1anisotropicsample_conditions_2
2D DQF-COSYsample_1anisotropicsample_conditions_2
2D NOESYsample_1anisotropicsample_conditions_2
2D 1H-31P hetcorsample_1anisotropicsample_conditions_2

Software:

SPARKY, Goddard - chemical shift assignment, peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMR spectrometers:

  • Agilent DD2 600 MHz
  • Agilent DD2 500 MHz

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