BMRB Entry 30253

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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/BMR30253
MolProbity Validation Chart

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Title:
Insights into Watson-Crick/Hoogsteen Breathing Dynamics and Damage Repair from the Solution Structure and Dynamic Ensemble of DNA Duplexes containing m1A - A2-DNA structure
Deposition date:
2017-02-26
Original release date:
2017-04-03
Authors:
Sathyamoorthy, B.; Shi, H.; Xue, Y.; Al-Hashimi, H.
Citation:

Citation: Sathyamoorthy, B.; Shi, H.; Zhou, H.; Xue, Y.; Rangadurai, A.; Merriman, D.; Al-Hashimi, H.. "Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A"  Nucleic Acids Res. 45, 5586-5601 (2017).
PubMed: 28369571

Assembly members:

Assembly members:
entity_1, polymer, 12 residues, 3678.403 Da.
entity_2, polymer, 12 residues, 3647.393 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: 32630   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):
entity_1: GCATCGATTGGC
entity_2: GCCAATCGATGC

Data sets:
Data typeCount
13C chemical shifts113
15N chemical shifts10
1H chemical shifts155
31P chemical shifts22

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 12 residues - 3678.403 Da.

1   DGDCDADTDCDGDADTDTDG
2   DGDC

Entity 2, entity_2 12 residues - 3647.393 Da.

1   DGDCDCDADADTDCDGDADT
2   DGDC

Samples:

sample_1: DNA (5'-D(*GP*CP*AP*TP*CP*GP*AP*TP*TP*GP*GP*C)-3') 3.25 ± 0.25 mM; DNA (5'-D(*GP*CP*CP*AP*AP*TP*CP*GP*AP*TP*GP*C)-3') 3.25 ± 0.25 mM; sodium phosphate buffer 15 mM; sodium chloride 25 mM; EDTA 0.1 mM

sample_2: DNA (5'-D(*GP*CP*AP*TP*CP*GP*AP*TP*TP*GP*GP*C)-3') 3.25 ± 0.25 mM; DNA (5'-D(*GP*CP*CP*AP*AP*TP*CP*GP*AP*TP*GP*C)-3') 3.25 ± 0.25 mM; sodium phosphate buffer 15 mM; sodium chloride 25 mM; EDTA 0.1 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 100 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N SOFAST-HMQCsample_1isotropicsample_conditions_1
2D 1H-13C SOFAST-HMQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-31P HSQCsample_1isotropicsample_conditions_1
2D 1H-13C TROSYsample_1isotropicsample_conditions_1
2D 1H-13C TROSYsample_2anisotropicsample_conditions_2

Software:

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

SPARKY vNMRFAM, Goddard - chemical shift assignment, peak picking

TOPSPIN, Bruker Biospin - collection

VNMR, Varian - collection

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

NMR spectrometers:

  • Varian INOVA 800 MHz
  • Bruker AvanceII 600 MHz