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PDBsum entry 1nkd
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Transcription regulation
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PDB id
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1nkd
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References listed in PDB file
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Key reference
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Title
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Structural parameters for proteins derived from the atomic resolution (1.09 a) structure of a designed variant of the cole1 rop protein.
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Authors
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M.Vlassi,
Z.Dauter,
K.S.Wilson,
M.Kokkinidis.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1998,
54,
1245-1260.
[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
percentage match of
85%.
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Abstract
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The crystal structure of a designed variant of the ColE1 repressor of primer
(ROP) protein has been refined with SHELXL93 to a resolution of 1.09 A. The
final model with 510 non-H protein atoms, 576 H atoms in calculated positions
and 114 water molecules converged to a standard R factor of 10% using
unrestrained blocked full-matrix refinement. For all non-H atoms six-parameter
anisotropic thermal parameters have been refined. The majority of atomic
vibrations have a preferred orientation which is approximately perpendicular to
the bundle axis; analysis with the TLS method [Schomaker & Trueblood (1968).
Acta Cryst. B24, 63-77] showed a relatively good agreement between the
individual atomic displacements and a rigid-body motion of the protein.
Disordered residues with multiple conformations form clusters on the surface of
the protein; six C-terminal residues have been omitted from the refined model
due to disorder. Part of the solvent structure forms pentagonal or hexagonal
clusters which bridge neighbouring protein molecules. Some water molecules are
also conserved in wild-type ROP. The unrestrained blocked full-matrix
least-squares refinement yielded reliable estimates of the standard deviations
of the refined parameters. Comparison of these parameters with the
stereochemical restraints used in various protein refinement programs showed
statistically significant differences. These restraints should be adapted to the
refinement of macromolecules by taking into account parameters determined from
atomic resolution protein structures.
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Figure 1.
Figure 1 Schematic representation of the structure of  aa}\rangle]
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Figure 2.
Figure 2 Course of the R factors during the refinement of aa}\rangle]
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1998,
54,
1245-1260)
copyright 1998.
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Secondary reference #1
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Title
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Restored heptad pattern continuity does not alter the folding of a four-Alpha-Helix bundle.
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Authors
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M.Vlassi,
C.Steif,
P.Weber,
D.Tsernoglou,
K.S.Wilson,
H.J.Hinz,
M.Kokkinidis.
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Ref.
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Nat Struct Biol, 1994,
1,
706-716.
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PubMed id
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Secondary reference #2
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Title
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Correlation between protein stability and crystal properties of designed rop variants.
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Authors
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M.Kokkinidis,
M.Vlassi,
Y.Papanikolaou,
D.Kotsifaki,
A.Kingswell,
D.Tsernoglou,
H.J.Hinz.
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Ref.
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Proteins, 1993,
16,
214-216.
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PubMed id
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Secondary reference #3
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Title
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Structure of the cole1 rop protein at 1.7 a resolution.
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Authors
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D.W.Banner,
M.Kokkinidis,
D.Tsernoglou.
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Ref.
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J Mol Biol, 1987,
196,
657-675.
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PubMed id
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