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PDBsum entry 1da3
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References listed in PDB file
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Key reference
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Title
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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.
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Authors
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I.Baikalov,
K.Grzeskowiak,
K.Yanagi,
J.Quintana,
R.E.Dickerson.
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Ref.
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J Mol Biol, 1993,
231,
768-784.
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
perfect match.
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Abstract
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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.
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Secondary reference #1
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Title
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The structure of b-Helical c-G-A-T-C-G-A-T-C-G and comparison with c-C-A-A-C-G-T-T-G-G. The effect of base pair reversals.
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Authors
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K.Grzeskowiak,
K.Yanagi,
G.G.Privé,
R.E.Dickerson.
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Ref.
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J Biol Chem, 1991,
266,
8861-8883.
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PubMed id
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Headers
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