3V9D image
Deposition Date 2011-12-26
Release Date 2012-04-18
Last Version Date 2024-04-03
Entry Detail
PDB ID:
3V9D
Keywords:
DNA
Title:
Crystal structure of the tetra-decanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex
Biological Source:
Source Organism:
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.50 Å
R-Value Free:
0.24
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 41
3V9D validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*CP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*GP*G)-3')
Chain IDs:A, B
Chain Length:14
Number of Molecules:2
Biological Source:
Ligand Molecules
MN
Primary Citation
Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex
Acta Crystallogr.,Sect.F 68 393 399 (2012)
PMID: 22505405 DOI: 10.1107/S174430911200869X

Abstact

The crystal structure of the tetradecanucleotide sequence d(CCCCGGTACCGGGG)(2) has been determined at 2.5 Å resolution in the tetragonal space group P4(1). This sequence was designed with the expectation of a four-way junction. However, the sequence crystallized as an A-DNA duplex and represents more than one full turn of the A-helix. The crystallographic asymmetric unit consists of one tetradecanucleotide duplex. The structural parameters of the A-type DNA duplex structure and the crystal-packing arrangement are described. One Mn(2+) ion was identified with direct coordination to the N7 position of G(13) and a water molecule at the major-groove side of the C(2)·G(13) base pair.

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Primary Citation of related structures
3QK4