BMRB Entry 11608

Name: SOLUTION STRUCTURE OF DNA CONTAINING METALLO-BASE-PAIR
Published: 2016-08-22

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PDB ID: 2rvp
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR11608
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

SOLUTION STRUCTURE OF DNA CONTAINING METALLO-BASE-PAIR

Deposition date:

2016-03-22

Original release date:

2016-08-22

Authors:

Dairaku, Takenori; Furuita, Kyoko; Sato, Hajime; Sebera, Jakub; Nakashima, Katsuyuki; Kondo, Jiro; Yamanaka, Daichi; Kondo, Yoshinori; Okamoto, Itaru; Ono, Akira; Sychrovsky, Vladimir; Kojima, Chojiro; Tanaka, Yoshiyuki

Citation:

Citation: Dairaku, Takenori; Furuita, Kyoko; Sato, Hajime; Sebera, Jakub; Nakashima, Katsuyuki; Kondo, Jiro; Yamanaka, Daichi; Kondo, Yoshinori; Okamoto, Itaru; Ono, Akira; Sychrovsky, Vladimir; Kojima, Chojiro; Tanaka, Yoshiyuki. "Structure Determination of an AgI-Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with 1H/15N/109Ag NMR Spectroscopy" Chem. Eur. J. ., .-. (2016).
PubMed: 27505707

Assembly members:

Assembly members:
DNA_(5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3'), polymer, 15 residues, 4566.059 Da.
DNA_(5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3'), polymer, 15 residues, 4566.059 Da.
SILVER ION, non-polymer, 107.868 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available 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):
DNA_(5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3'): TAATATACTTAATTA
DNA_(5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3'): TAATTAACTATATTA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	244

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (5'-D(TPAPAPTPAPTPAPCPTPTPAPAPTPTP*A)-3')	1
2	DNA (5'-D(TPAPAPTPTPAPAPCPTPAPTPAPTPTP*A)-3')	2
3	SILVER ION	3

Entities:

Entity 1, DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3') 15 residues - 4566.059 Da.

1

DT

DA

DT

DA

DT

DA

DC

DT

2

DA

DT

DA

Entity 2, DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3') 15 residues - 4566.059 Da.

1

DT

DA

DT

DA

DC

DT

DA

2

DT

DA

DT

DA

Entity 3, SILVER ION - Ag - 107.868 Da.

1

AG

Samples:

sample_1: DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3') 2 mM; DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3') 2 mM; AgNO3 2.1 mM; NaNO3 100 mM; H2O 90%; D2O, [U-2H], 10%

sample_2: DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3') 2 mM; DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3') 2 mM; AgNO3 2.1 mM; NaNO3 100 mM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 0.1 M; pH: 6.9; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.1 M; pH: 7.1; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D DQF-COSY	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_2

Software:

SPARKY, Goddard - chemical shift assignment, peak picking

MARDIGRAS, Thomas L. James - data analysis, structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

NMR spectrometers:

Bruker Avance 950 MHz