137D

A-DNA DECAMER D(GCGGGCCCGC)-ORTHORHOMBIC CRYSTAL FORM

Summary for 137D

• Entry DOI: 10.2210/pdb137d/pdb
• Descriptor: DNA (5'-D(*GP*CP*GP*GP*GP*CP*CP*CP*GP*C)-3') (2 entities in total)
• Functional Keywords: a-dna, double helix, dna
• Total number of polymer chains: 2
• Total formula weight: 6093.96

Authors

Ramakrishnan, B.,Sundaralingam, M. (deposition date: 1993-09-15, release date: 1994-01-15, Last modification date: 2024-02-07)

Primary citation

Ramakrishnan, B.,Sundaralingam, M.
Evidence for crystal environment dominating base sequence effects on DNA conformation: crystal structures of the orthorhombic and hexagonal polymorphs of the A-DNA decamer d(GCGGGCCCGC) and comparison with their isomorphous crystal structures.
Biochemistry, 32:11458-11468, 1993

PubMed Abstract: We have determined the structure of the A-DNA decamer d(GCGGGCCCGC) in two crystal forms, orthorhombic and hexagonal, at 1.7- and 1.8-A resolution, respectively. In the orthorhombic form, the fifth guanine residue has nearly trans-trans conformations for the alpha-gamma backbone torsions, as in the isomorphous orthorhombic structure d(CCCGGCCGGG) [Ramakrishnan, B., & Sundaralingam, M. (1993) J. Mol. Biol. 231, 431-444]. However, in the hexagonal form, the eighth cytosine residue adopts the trans-trans conformations for the backbone alpha-gamma torsions, as in the isomorphous hexagonal structure d(ACCGGCCGGT) [Frederick, C. A., Quigley, G. J., Teng, M.-K., Coll, M., van der Marel, G. A., van Boom, J. H., Rich, A., & Wang, A. H.-J. (1989) Eur. J. Biochem. 181, 295-307]. Even though the average helix and base-pair parameters are nearly the same in the two polymorphous crystal forms having the same sequence, many of the base-dependent local helix parameters are quite different. However, in the isomorphous crystal forms, in spite of the differing base sequences, the local helix and base-pair parameters of the duplexes are nearly the same. This indicates that, in crystals, the local conformation of a DNA structure is affected severely by the crystal packing environment rather than by the base sequence.

PubMed: 8218212
DOI: 10.1021/bi00093a025

Experimental method

X-RAY DIFFRACTION (1.7 Å)