1vj4: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image:1vj4.gif|left|200px]] | [[Image:1vj4.gif|left|200px]] | ||
'''SEQUENCE-DEPENDENT CONFORMATION OF AN A-DNA DOUBLE HELIX: THE CRYSTAL STRUCTURE OF THE OCTAMER D(G-G-T-A-T-A-C-C)''' | {{Structure | ||
|PDB= 1vj4 |SIZE=350|CAPTION= <scene name='initialview01'>1vj4</scene>, resolution 1.800Å | |||
|SITE= | |||
|LIGAND= | |||
|ACTIVITY= | |||
|GENE= | |||
}} | |||
'''SEQUENCE-DEPENDENT CONFORMATION OF AN A-DNA DOUBLE HELIX: THE CRYSTAL STRUCTURE OF THE OCTAMER D(G-G-T-A-T-A-C-C)''' | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
1VJ4 is a [ | 1VJ4 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VJ4 OCA]. | ||
==Reference== | ==Reference== | ||
Sequence-dependent conformation of an A-DNA double helix. The crystal structure of the octamer d(G-G-T-A-T-A-C-C)., Shakked Z, Rabinovich D, Kennard O, Cruse WB, Salisbury SA, Viswamitra MA, J Mol Biol. 1983 May 15;166(2):183-201. PMID:[http:// | Sequence-dependent conformation of an A-DNA double helix. The crystal structure of the octamer d(G-G-T-A-T-A-C-C)., Shakked Z, Rabinovich D, Kennard O, Cruse WB, Salisbury SA, Viswamitra MA, J Mol Biol. 1983 May 15;166(2):183-201. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/6854642 6854642] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Cruse, W B.]] | [[Category: Cruse, W B.]] | ||
| Line 21: | Line 30: | ||
[[Category: double helix]] | [[Category: double helix]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:46:18 2008'' | ||
Revision as of 12:46, 20 March 2008
| |||||||||||||
| 1vj4, resolution 1.800Å | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
SEQUENCE-DEPENDENT CONFORMATION OF AN A-DNA DOUBLE HELIX: THE CRYSTAL STRUCTURE OF THE OCTAMER D(G-G-T-A-T-A-C-C)
Overview
The crystal structures of the synthetic self-complementary octamer d(G-G-T-A-T-A-C-C) and its 5-bromouracil-containing analogue have been refined to R values of 20% and 14% at resolutions of 1.8 and 2.25 A, respectively. The molecules adopt and A-DNA type double-helical conformation, which is minimally affected by crystal forces. A detailed analysis of the structure shows a considerable influence of the nucleotide sequence on the base-pair stacking patterns. In particular, the electrostatic stacking interactions between adjacent guanine and thymine bases produce symmetric bending of the double helix and a major-groove widening. The sugar-phosphate backbone appears to be only slightly affected by the base sequence. The local variations in the base-pair orientation are brought about by correlated adjustments in the backbone torsion angles and the glycosidic orientation. Sequence-dependent conformational variations of the type observed here may contribute to the specificity of certain protein-DNA interactions.
About this Structure
1VJ4 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Sequence-dependent conformation of an A-DNA double helix. The crystal structure of the octamer d(G-G-T-A-T-A-C-C)., Shakked Z, Rabinovich D, Kennard O, Cruse WB, Salisbury SA, Viswamitra MA, J Mol Biol. 1983 May 15;166(2):183-201. PMID:6854642
Page seeded by OCA on Thu Mar 20 14:46:18 2008
