BMRB Entry 30015

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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/BMR30015
MolProbity Validation Chart

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Title:
DNA duplex containing a ribonolactone lesion
Deposition date:
2016-01-21
Original release date:
2016-09-09
Authors:
Zalesak, J.; Constant, J.; Jourdan, M.
Citation:

Citation: Zalesak, J.; Constant, J.; Jourdan, M.. "Nuclear Magnetic Resonance Solution Structure of DNA Featuring Clustered 2'-Deoxyribonolactone and 8-Oxoguanine Lesions"  Biochemistry 55, 3899-3906 (2016).
PubMed: 27322640

Assembly members:

Assembly members:
entity_1, polymer, 11 residues, 3160.024 Da.
entity_2, polymer, 11 residues, 3471.246 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: CGCTCXCACGC
entity_2: GCGTGGGAXCG

Data sets:
Data typeCount
1H chemical shifts190

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 11 residues - 3160.024 Da.

1   DCDGDCDTDC63TDCDADCDG
2   DC

Entity 2, entity_2 11 residues - 3471.246 Da.

1   DGDCDGDTDGDGDGDA8OGDC
2   DG

Samples:

sample_1: entity_1, none, 0.85 mM; entity_2, none, 0.85 mM; NaCl 100 mM; sodium phosphate buffer 20 mM

sample_2: entity_1, none, 0.85 mM; entity_2, none, 0.85 mM; NaCl 100 mM; sodium phosphate buffer 20 mM

sample_conditions_1: ionic strength: 120 mM; pH: 6; pressure: 1 bar; temperature: 283 K

Experiments:

NameSampleSample stateSample conditions
2D NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1

Software:

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

CcpNMR, CCPN - chemical shift assignment

NMR spectrometers:

  • Bruker AvanceIII 500 MHz