1ZFF

TTC Duplex B-DNA

Summary for 1ZFF

• Entry DOI: 10.2210/pdb1zff/pdb
• Related: 1DCV 1DCW 1P4Y 1P4Z 1ZEW 1ZEX 1ZEY 1ZEZ 1ZF0 1ZF1 1ZF2 1ZF3 1ZF4 1ZF5 1ZF6 1ZF7 1ZF8 1ZF9 1ZFA 1ZFB 1ZFC 1ZFE 1ZFG 1ZFH 1ZFM
• Descriptor: 5'-D(*CP*CP*GP*AP*AP*TP*TP*CP*GP*G)-3' (1 entity in total)
• Functional Keywords: crystallographic screen, dna structure, holliday junction, molecular structure, dna
• Total number of polymer chains: 1
• Total formula weight: 3045.01

Authors

Hays, F.A.,Teegarden, A.T.,Jones, Z.J.R.,Harms, M.,Raup, D.,Watson, J.,Cavaliere, E.,Ho, P.S. (deposition date: 2005-04-20, release date: 2005-05-10, Last modification date: 2024-04-03)

Primary citation

Hays, F.A.,Teegarden, A.,Jones, Z.J.,Harms, M.,Raup, D.,Watson, J.,Cavaliere, E.,Ho, P.S.
How sequence defines structure: a crystallographic map of DNA structure and conformation.
Proc.Natl.Acad.Sci.Usa, 102:7157-7162, 2005

PubMed Abstract: The fundamental question of how sequence defines conformation is explicitly answered if the structures of all possible sequences of a macromolecule are determined. We present here a crystallographic screen of all permutations of the inverted repeat DNA sequence d(CCnnnN6N7N8GG), where N6, N7, and N8 are any of the four naturally occurring nucleotides. At this point, 63 of the 64 possible permutations have been crystallized from a defined set of solutions. When combined with previous work, we have assembled a data set of 37 single-crystal structures from 29 of the sequences in this motif, representing three structural classes of DNA (B-DNA, A-DNA, and four-stranded Holliday junctions). This data set includes a unique set of amphimorphic sequence, those that crystallize in two different conformations and serve to bridge the three structural phases. We have thus constructed a map of DNA structures that can be walked through in single nucleotide steps. Finally, the resulting data set allows us to dissect in detail the stabilization of and conformational variations within structural classes and identify significant conformational deviations within a particular structural class that result from sequence rather than crystal or crystallization effects.

PubMed: 15870206
DOI: 10.1073/pnas.0409455102

Experimental method

X-RAY DIFFRACTION (0.94 Å)