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 16834

Title: NMR structure of fully methylated GATC site   PubMed: 19108701

Authors: Bang, Jongchul; Bae, Sung-Hun; Park, Chin-Ju; Lee, Joon-Hwa; Choi, Byong-Seok

Citation: Bang, Jongchul; Bae, Sung-Hun; Park, Chin-Ju; Lee, Joon-Hwa; Choi, Byong-Seok. "Structural and dynamics study of DNA dodecamer duplexes that contain un-, hemi-, or fully methylated GATC sites."  J. Am. Chem. Soc. 130, 17688-17696 (2008).

Assembly members:
DNA_1, polymer, 12 residues, 3717.473 Da.
DNA_2, polymer, 12 residues, 3637.424 Da.

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:   Production method: recombinant technology   Host organism: chemical synthesis

Entity Sequences (FASTA):
DNA_1: GCGAGATCTGCG
DNA_2: CGCAGATCTCGC

Data sets:
Data typeCount
1H chemical shifts137

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA GCGAGATCTGCG1
2DNA CGCAGATCTCGC2

Entities:

Entity 1, DNA GCGAGATCTGCG 12 residues - 3717.473 Da.

1   DGDCDGDADGDADTDCDTDG
2   DCDG

Entity 2, DNA CGCAGATCTCGC 12 residues - 3637.424 Da.

1   DCDGDCDADGDADTDCDTDC
2   DGDC

Samples:

dynamics: DNA GCGAGATCTGCG0.5 – 1.0 mM; DNA CGCAGATCTCGC0.5 – 1.0 mM; H2O 90%; D2O 10%

structure: DNA GCGAGATCTGCG0.5 – 1.0 mM; DNA CGCAGATCTCGC0.5 – 1.0 mM; D2O 100%

structure_14c: pH: 6.8; temperature: 287 K

structure_35c: pH: 6.8; temperature: 308 K

structure_30c: pH: 6.8; temperature: 303 K

structure_15c: pH: 6.8; temperature: 288 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYstructureisotropicstructure_14c
2D 1H-1H COSYstructureisotropicstructure_14c
2D 1H-1H TOCSYstructureisotropicstructure_14c
2D 1H-13C HSQCstructureisotropicstructure_30c
2D 1H-13C HSQCstructureanisotropicstructure_30c
2D 1H-1H NOESYdynamicsisotropicstructure_15c
2D 1H-1H NOESYdynamicsisotropicstructure_35c

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

SPARKY, Goddard - chemical shift assignment, peak picking

FELIX, Accelrys Software Inc. - data analysis

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

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

VNMRJ, Varian - collection

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Varian INOVA 900 MHz

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