BMRB Entry 16834
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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/BMR16834
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Title: NMR structure of fully methylated GATC site PubMed: 19108701
Deposition date: 2010-04-04 Original release date: 2010-07-27
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
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 137 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA GCGAGATCTGCG | 1 |
| 2 | DNA CGCAGATCTCGC | 2 |
Entities:
Entity 1, DNA GCGAGATCTGCG 12 residues - 3717.473 Da.
| 1 | DG | DC | DG | DA | DG | DA | DT | DC | DT | DG | ||||
| 2 | DC | DG |
Entity 2, DNA CGCAGATCTCGC 12 residues - 3637.424 Da.
| 1 | DC | DG | DC | DA | DG | DA | DT | DC | DT | DC | ||||
| 2 | DG | DC |
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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | structure | isotropic | structure_14c |
| 2D 1H-1H COSY | structure | isotropic | structure_14c |
| 2D 1H-1H TOCSY | structure | isotropic | structure_14c |
| 2D 1H-13C HSQC | structure | isotropic | structure_30c |
| 2D 1H-13C HSQC | structure | anisotropic | structure_30c |
| 2D 1H-1H NOESY | dynamics | isotropic | structure_15c |
| 2D 1H-1H NOESY | dynamics | isotropic | structure_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