BMRB Entry 11528

Name: STRUCTURE OF METALLO-DNA IN SOLUTION
Published: 2014-03-03

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PDB ID: 2rt8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR11528
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:

STRUCTURE OF METALLO-DNA IN SOLUTION

Deposition date:

2013-06-17

Original release date:

2014-03-03

Authors:

Yamaguchi, H.; Sebera, J.; Kondo, J.; Oda, S.; Komuro, T.; Kawamura, T.; Dairaku, T.; Kondo, Y.; Okamoto, I.; Ono, A.; Burda, J.; Kojima, C.; Sychrovsky, V.; Tanaka, Y.

Citation:

Citation: Yamaguchi, H.; Sebera, J.; Kondo, J.; Oda, S.; Komuro, T.; Kawamura, T.; Dairaku, T.; Kondo, Y.; Okamoto, I.; Ono, A.; Burda, J.; Kojima, C.; Sychrovsky, V.; Tanaka, Y.. "The structure of metallo-DNA with consecutive T-Hg(II)-T base-pairs explains positive entropy for the metallo-base-pair formation" .

Assembly members:

Assembly members:
5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3', polymer, 10 residues, 3011.991 Da.
5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3', polymer, 10 residues, 3061.029 Da.
MERCURY (II) ION, non-polymer, 200.590 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 Host organism: not applicable Vector: not applicable

Entity Sequences (FASTA):

Entity Sequences (FASTA):
5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3': CGCGTTGTCC
5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3': GGACTTCGCG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	220

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	5'-D(CPGPCPGPTPTPGPTPCPC)-3'	1
2	5'-D(GPGPAPCPTPTPCPGPCPG)-3'	2
3	MERCURY (II) ION_1	3
4	MERCURY (II) ION_2	3

Entities:

Entity 1, 5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3' 10 residues - 3011.991 Da.

1

DC

DG

DC

DG

DT

DG

DT

DC

Entity 2, 5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3' 10 residues - 3061.029 Da.

1

DG

DA

DC

DT

DC

DG

DC

DG

Entity 3, MERCURY (II) ION_1 - Hg - 200.590 Da.

1

HG

Samples:

sample_1: 5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3' 2.0 mM; 5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3' 2.0 mM; Mercury(II) perchlorate 4.0 mM; Sodium perchlorate 100 mM; D2O, [U-100% 2H], 100%

sample_2: 5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3' 2.0 mM; 5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3' 2.0 mM; Mercury(II) perchlorate 4.0 mM; Sodium perchlorate 100 mM; H2O 95%; D2O, [U-100% 2H], 5%

sample_conditions_1: ionic strength: 0.10 M; pH: 6.0; pressure: 1 atm; temperature: 293 K

sample_conditions_2: ionic strength: 0.10 M; pH: 6.0; pressure: 1 atm; temperature: 283 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_1	isotropic	sample_conditions_1

Software:

X-PLOR v3.851, A. T. BRUNGER - refinement, structure solution

SPARKY v3.1, Goddard - chemical shift assignment, peak picking, processing

MARDIGRAS, Thomas L. James - structure solution

NMR spectrometers:

BRUKER DRX800 800 MHz