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 30038

Title: Solution Structure of DNA Dodecamer with 8-oxoguanine at 4th Position

Authors: Miears, H.; Gruber, D.; Hoppins, J.; Kiryutin, A.; Kasymov, R.; Yurkovskaya, A.; Zharkov, D.; Smirnov, S.

Citation: Miears, H.; Gruber, D.; Hoppins, J.; Kiryutin, A.; Kasymov, R.; Yurkovskaya, A.; Zharkov, D.; Smirnov, S.. "Structure of 8-oxoguanine in the EcoRI recognition site and loss of EcoRI function/recognition."  . ., .-..

Assembly members:
DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*CP*GP*CP*G)-3'), polymer, 12 residues, 3679.392 Da.

Natural source:   Common Name: not available   Taxonomy ID: 32630   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*CP*GP*CP*G)-3'): CGCXAATTCGCG

Data typeCount
1H chemical shifts186
31P chemical shifts14

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_1, chain 11
2entity_1, chain 21

Entities:

Entity 1, entity_1, chain 1 12 residues - 3679.392 Da.

1   DCDGDC8OGDADADTDTDCDG
2   DCDG

Samples:

sample_1: DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*CP*GP*CP*G)-3') 0.2 mM; EDTA 1 mM; potassium phosphate 10 mM; sodium chloride 50 mM; D2O 100%

sample_conditions_1: ionic strength: 120 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 120 mM; pH: 6.8; pressure: 1 atm; temperature: 278 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_2
2D DQF-COSYsample_1isotropicsample_conditions_1
31P HETCORsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1

Software:

AMBER v12, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - refinement, structure calculation

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - data analysis

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v9.0, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

  • Bruker Avance 700 MHz

Related Database Links: