1da3
From Proteopedia
(New page: 200px<br /><applet load="1da3" size="450" color="white" frame="true" align="right" spinBox="true" caption="1da3, resolution 2.000Å" /> '''THE CRYSTAL STRUCTU...) |
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| - | [[Image:1da3.gif|left|200px]]<br /><applet load="1da3" size=" | + | [[Image:1da3.gif|left|200px]]<br /><applet load="1da3" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1da3, resolution 2.000Å" /> | caption="1da3, resolution 2.000Å" /> | ||
'''THE CRYSTAL STRUCTURE OF THE TRIGONAL DECAMER C-G-A-T-C-G-6MEA-T-C-G: A B-DNA HELIX WITH 10.6 BASE-PAIRS PER TURN'''<br /> | '''THE CRYSTAL STRUCTURE OF THE TRIGONAL DECAMER C-G-A-T-C-G-6MEA-T-C-G: A B-DNA HELIX WITH 10.6 BASE-PAIRS PER TURN'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The B-DNA decanucleotide C-G-A-T-C-G-6meA-T-C-G has been crystallized | + | The B-DNA decanucleotide C-G-A-T-C-G-6meA-T-C-G has been crystallized under the same conditions used earlier for C-G-A-T-C-G-A-T-C-G, but is found to adopt a new trigonal P3(2)21 packing mode instead of the expected orthorhombic P2(1)2(1)2(1) form. Unit cell dimensions a = b = 33.38 A, c = 98.30 A, gamma = 120 degrees, imply ten base-pairs or one complete decamer double helix per asymmetric unit. The 2282 two-sigma data to 2.0 A refine to R = 17.2% with 45 water molecules, 1.5 hexavalent hydrated magnesium complexes, and 0.5 chloride ion per asymmetric unit. Neighboring helices interlock backbone chains and major grooves, crossing at an angle of 120 degrees in a manner that yields an excellent model for a Holliday junction. Local helix parameters differ markedly in the trigonal and orthorhombic structures, with the trigonal helix exhibiting behavior closer to that expected of B-DNA in solution. The trigonal form has an average of 10.6 base-pairs per turn, in contrast to 9.7 base-pairs per turn in the orthorhombic cell. A comparison of all known B-DNA decamer and dodecamer crystal structure analyses indicates that, the greater the cell volume per base-pair (and hence the more open the crystal structure), the closer the mean helix twist approaches an expected 10.6 base-pairs per turn. |
==About this Structure== | ==About this Structure== | ||
| - | 1DA3 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with CL and MG as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1DA3 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DA3 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Baikalov, I.]] | [[Category: Baikalov, I.]] | ||
| - | [[Category: Dickerson, R | + | [[Category: Dickerson, R E.]] |
[[Category: Grzeskowiak, K.]] | [[Category: Grzeskowiak, K.]] | ||
[[Category: Quintana, J.]] | [[Category: Quintana, J.]] | ||
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[[Category: modified]] | [[Category: modified]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:14:35 2008'' |
Revision as of 10:14, 21 February 2008
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THE CRYSTAL STRUCTURE OF THE TRIGONAL DECAMER C-G-A-T-C-G-6MEA-T-C-G: A B-DNA HELIX WITH 10.6 BASE-PAIRS PER TURN
Overview
The B-DNA decanucleotide C-G-A-T-C-G-6meA-T-C-G has been crystallized under the same conditions used earlier for C-G-A-T-C-G-A-T-C-G, but is found to adopt a new trigonal P3(2)21 packing mode instead of the expected orthorhombic P2(1)2(1)2(1) form. Unit cell dimensions a = b = 33.38 A, c = 98.30 A, gamma = 120 degrees, imply ten base-pairs or one complete decamer double helix per asymmetric unit. The 2282 two-sigma data to 2.0 A refine to R = 17.2% with 45 water molecules, 1.5 hexavalent hydrated magnesium complexes, and 0.5 chloride ion per asymmetric unit. Neighboring helices interlock backbone chains and major grooves, crossing at an angle of 120 degrees in a manner that yields an excellent model for a Holliday junction. Local helix parameters differ markedly in the trigonal and orthorhombic structures, with the trigonal helix exhibiting behavior closer to that expected of B-DNA in solution. The trigonal form has an average of 10.6 base-pairs per turn, in contrast to 9.7 base-pairs per turn in the orthorhombic cell. A comparison of all known B-DNA decamer and dodecamer crystal structure analyses indicates that, the greater the cell volume per base-pair (and hence the more open the crystal structure), the closer the mean helix twist approaches an expected 10.6 base-pairs per turn.
About this Structure
1DA3 is a Protein complex structure of sequences from [1] with and as ligands. Full crystallographic information is available from OCA.
Reference
The crystal structure of the trigonal decamer C-G-A-T-C-G-6meA-T-C-G: a B-DNA helix with 10.6 base-pairs per turn., Baikalov I, Grzeskowiak K, Yanagi K, Quintana J, Dickerson RE, J Mol Biol. 1993 Jun 5;231(3):768-84. PMID:8515450
Page seeded by OCA on Thu Feb 21 12:14:35 2008
Categories: Protein complex | Baikalov, I. | Dickerson, R E. | Grzeskowiak, K. | Quintana, J. | Yanagi, K. | CL | MG | B-dna | Double helix | Modified
