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PDBsum entry 123d
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References listed in PDB file
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Key reference
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Title
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Dna helix structure and refinement algorithm: comparison of models for d(ccaggcm5ctgg) derived from nuclsq, Tnt and x-Plor.
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Authors
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M.Hahn,
U.Heinemann.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1993,
49,
468-477.
[DOI no: ]
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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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In an earlier study [Heinemann & Hahn (1992). J. Biol. Chem. 267,
7332-7341], the crystal structure of the double-stranded B-DNA decamer
d(CCAGGCm(5)CTGG) was refined with NUCLSQ to R = 17.4% against 3799 2sigma
structure amplitudes in the resolution range 8-1.7 A. This structure has now
been re-refined against the same diffraction data using either TNT or X-PLOR in
order to determine to what extent the resulting DNA conformations would differ
and to examine the suitability of these programs for the refinement of
oligonucleotide structures. The R value from the NUCLSQ refinement could not be
reached with either TNT or X-PLOR, although both programs yield reasonably
refined DNA models showing root-mean-square deviations against the NUCLSQ model
of the decamer duplex of 0.25 and 0.32 A, respectively. Some derived local
structure parameters differ depending on the refinement procedure used. This
holds true for several exocyclic torsion angles of the sugar-phosphate backbone,
whereas sugar puckers as well as helical and base-pair stacking parameters are
only weakly influenced. A subset of 15 solvent sites with low temperature
factors is conserved in all three models.
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Figure 1.
Fig. 1. Portions of the
2Fo-Fc
difference electron-density maps
around base pair A(3).T(18) of d(CCAGGCmSCTGG). The
maps are contoured at 1.5 times their r.m.s, density. Models and
maps are derived from (a)
NUCLSQ, (b) TNT
and (c)
X-PLOR.
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Figure 5.
Fig. 5. Average temperature factors (A
2) for the atoms in
bases (B), sugars (S) and phosphate groups (P) of
d(CCAGGCmSCTGG) after refinement with
NUCLSQ
(yellow),
TNT
(red) and
X-PLOR
(blue).
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1993,
49,
468-477)
copyright 1993.
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Secondary reference #1
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Title
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C-C-A-G-G-C-M5c-T-G-G. Helical fine structure, Hydration, And comparison with c-C-A-G-G-C-C-T-G-G.
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Authors
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U.Heinemann,
M.Hahn.
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Ref.
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J Biol Chem, 1992,
267,
7332-7341.
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PubMed id
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Secondary reference #2
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Title
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Double helix conformation, Groove dimensions and ligand binding potential of a g/c stretch in b-Dna.
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Authors
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U.Heinemann,
C.Alings,
M.Bansal.
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Ref.
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Embo J, 1992,
11,
1931-1939.
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PubMed id
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Secondary reference #3
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Title
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The conformation of a b-Dna decamer is mainly determined by its sequence and not by crystal environment.
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Authors
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U.Heinemann,
C.Alings.
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Ref.
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Embo J, 1991,
10,
35-43.
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PubMed id
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Secondary reference #4
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Title
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Crystallographic study of one turn of g/c-Rich b-Dna.
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Authors
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U.Heinemann,
C.Alings.
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Ref.
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J Mol Biol, 1989,
210,
369-381.
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PubMed id
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Headers
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