BMRB Entry 16834

Name: NMR structure of fully methylated GATC site
Published: 2010-07-27

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PDB ID: 2kal
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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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR structure of fully methylated GATC site

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:

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).
PubMed: 19108701

Assembly members:

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

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: chemical synthesis Vector: not applicable

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	137

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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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