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 34245

Title: Concerted dynamics of metallo-base pairs in an A/B-form helical transition (minor species)   PubMed: 31645548

Authors: Schmidt, O.; Jurt, S.; Johannsen, S.; Karimi, A.; Sigel, R.; Luedtke, N.

Citation: Schmidt, O.; Jurt, S.; Johannsen, S.; Karimi, A.; Sigel, R.; Luedtke, N.. "Concerted dynamics of metallo-base pairs in an A/B-form helical transition"  Nat. Commun. 10, 4818-4818 (2019).

Assembly members:
DNA (5'-D(*CP*GP*TP*CP*TP*CP*AP*TP*GP*AP*TP*AP*CP*G)-3')_minor, polymer, 14 residues, 4255.778 Da.
MERCURY (II) ION, non-polymer, 200.590 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*TP*CP*TP*CP*AP*TP*GP*AP*TP*AP*CP*G)-3')_minor: CGTCTCATGATACG

Data sets:
Data typeCount
1H chemical shifts150

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_1, 11
2entity_1, 21
3entity_2, 12
4entity_2, 22

Entities:

Entity 1, entity_1, 1 14 residues - 4255.778 Da.

1   DCDGDTDCDTDCDADTDGDA
2   DTDADCDG

Entity 2, entity_2, 1 - Hg - 200.590 Da.

1   HG

Samples:

sample_1: polydeoxyribonucleotide 0.4 mM; MERCURY (II) ION 1.2 mM

sample_conditions_1: ionic strength: 50 mM; pH: 7.35 pD; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment, peak picking

XPLOR-NIH v2.46, G. Marius Clore, Guillermo Bermejo, John Kuszewski, Charles D. Schwieters, and Nico Tjandra - refinement, structure calculation

TOPSPIN v4.0.0.b.16, Bruker Biospin - collection

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 700 MHz

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