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1d16
From Proteopedia
(New page: 200px<br /><applet load="1d16" size="450" color="white" frame="true" align="right" spinBox="true" caption="1d16, resolution 2.100Å" /> '''STRUCTURE OF A T4 H...) |
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| - | [[Image:1d16.gif|left|200px]]<br /><applet load="1d16" size=" | + | [[Image:1d16.gif|left|200px]]<br /><applet load="1d16" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1d16, resolution 2.100Å" /> | caption="1d16, resolution 2.100Å" /> | ||
'''STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS'''<br /> | '''STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The synthetic DNA oligomer C-G-C-G-C-G-T-T-T-T-C-G-C-G-C-G crystallizes as | + | The synthetic DNA oligomer C-G-C-G-C-G-T-T-T-T-C-G-C-G-C-G crystallizes as a Z-DNA hexamer, capped at one end by a T4 loop. The crystals are monoclinic, space group C2, with a = 57.18 A, b = 21.63 A, c = 36.40 A, beta = 95.22 degrees, and one hairpin molecule per asymmetric unit. The structure of the z-hexamer stem was determined by molecular replacement, and the T4 loop was positioned by difference map methods. The final R factor at 2.1 A resolution for hairpin plus 70 water molecules is 20% for 2 sigma data, with a root-mean-square error of 0.26 A. The (C-G)3 stem resembles the free Z-DNA hexamer with minor crystal packing effects. The T4 loop differs from that observed on a B-DNA stem in solution, or in longer loops in tRNA, in that it shows intraloop and intermolecular interactions rather than base stacking on the final base-pair of the stem. Bases T7, T8 and T9 stack with one another and with the sugar of T7. Two T10 bases from different molecules stack between the C1-G12 terminal base-pairs of a third and fourth molecule, to simulate a T.T "base-pair". Distances between thymine N and O atoms suggest that the two thymine bases are hydrogen bonded, and a keto-enol tautomer pair is favored over disordered keto-keto wobble pairs. The hairpin molecules pack in the crystal in herringbone columns in a manner that accounts well for the observed relative crystal growth rates in a, b and c directions. Hydration seems to be most extensive around the phosphate groups, with lesser hydration within the grooves. |
==About this Structure== | ==About this Structure== | ||
| - | 1D16 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 1D16 is a [http://en.wikipedia.org/wiki/Protein_complex 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=1D16 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Chattopadhyaya, R.]] | [[Category: Chattopadhyaya, R.]] | ||
| - | [[Category: Dickerson, R | + | [[Category: Dickerson, R E.]] |
[[Category: Grzeskowiak, K.]] | [[Category: Grzeskowiak, K.]] | ||
[[Category: hairpin loop]] | [[Category: hairpin loop]] | ||
| Line 19: | Line 19: | ||
[[Category: z-dna stem]] | [[Category: z-dna stem]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:11:51 2008'' |
Revision as of 10:11, 21 February 2008
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STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS
Overview
The synthetic DNA oligomer C-G-C-G-C-G-T-T-T-T-C-G-C-G-C-G crystallizes as a Z-DNA hexamer, capped at one end by a T4 loop. The crystals are monoclinic, space group C2, with a = 57.18 A, b = 21.63 A, c = 36.40 A, beta = 95.22 degrees, and one hairpin molecule per asymmetric unit. The structure of the z-hexamer stem was determined by molecular replacement, and the T4 loop was positioned by difference map methods. The final R factor at 2.1 A resolution for hairpin plus 70 water molecules is 20% for 2 sigma data, with a root-mean-square error of 0.26 A. The (C-G)3 stem resembles the free Z-DNA hexamer with minor crystal packing effects. The T4 loop differs from that observed on a B-DNA stem in solution, or in longer loops in tRNA, in that it shows intraloop and intermolecular interactions rather than base stacking on the final base-pair of the stem. Bases T7, T8 and T9 stack with one another and with the sugar of T7. Two T10 bases from different molecules stack between the C1-G12 terminal base-pairs of a third and fourth molecule, to simulate a T.T "base-pair". Distances between thymine N and O atoms suggest that the two thymine bases are hydrogen bonded, and a keto-enol tautomer pair is favored over disordered keto-keto wobble pairs. The hairpin molecules pack in the crystal in herringbone columns in a manner that accounts well for the observed relative crystal growth rates in a, b and c directions. Hydration seems to be most extensive around the phosphate groups, with lesser hydration within the grooves.
About this Structure
1D16 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structure of a T4 hairpin loop on a Z-DNA stem and comparison with A-RNA and B-DNA loops., Chattopadhyaya R, Grzeskowiak K, Dickerson RE, J Mol Biol. 1990 Jan 5;211(1):189-210. PMID:2299669
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