BMRB Entry 34328

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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/BMR34328
MolProbity Validation Chart

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Title:
Dodecamer DNA containing the synthetic base pair P-Z
Deposition date:
2018-11-10
Original release date:
2019-06-07
Authors:
Padroni, G.; Reichenbach, L.; Parkinson, J.; Burley, G.
Citation:

Citation: Padroni, G.; Withers, J.; Taladriz-Sender, A.; Reichenbach, L.; Parkinson, J.; Burley, G.. "Sequence-selective minor groove recognition of a DNA duplex containing synthetic genetic components."  J. Am. Chem. Soc. 141, 9555-9563 (2019).
PubMed: 31117639

Assembly members:

Assembly members:
entity_1, polymer, 12 residues, 3706.414 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: CGATXTAXATCG

Data sets:
Data typeCount
13C chemical shifts72
1H chemical shifts98
31P chemical shifts11

Additional metadata:

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

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

Entities:

Entity 1, entity_1, 1 12 residues - 3706.414 Da.

1   DCDGDADTDPDTDADZDADT
2   DCDG

Samples:

sample_1: ZP-DNA 1.3 mM

sample_2: ZP-DNA 1.3 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 100 mM; pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D 31P-1H COSYsample_1isotropicsample_conditions_1

Software:

Sparky, Goddard - chemical shift assignment

TopSpin, Bruker - processing

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

MARDIGRAS, Brandan A. Borgias; Paul D. Thomas; He Liu; Anil Kumar. - refinement

NMR spectrometers:

  • Bruker Avance II 600 MHz