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PDBsum entry 1kf8
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Atomic resolution structures of ribonuclease a at six ph values.
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Authors
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R.Berisio,
F.Sica,
V.S.Lamzin,
K.S.Wilson,
A.Zagari,
L.Mazzarella.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2002,
58,
441-450.
[DOI no: ]
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PubMed id
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Abstract
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The diffraction pattern of protein crystals extending to atomic resolution
guarantees a very accurate picture of the molecular structure and enables the
study of subtle phenomena related to protein functionality. Six structures of
bovine pancreatic ribonuclease at the pH* values 5.2, 5.9, 6.3, 7.1, 8.0 and 8.8
and at resolution limits in the range 1.05-1.15A have been refined. An overall
description of the six structures and several aspects, mainly regarding
pH-triggered conformational changes, are described here. Since subtle variations
were expected, a thorough validation assessment of the six refined models was
first carried out. Some stereochemical parameters, such as the
N[bond]C(alpha)[bond]C angle and the pyramidalization at the carbonyl C atoms,
indicate that the standard target values and their weights typically used in
refinement may need revision. A detailed comparison of the six structures has
provided experimental evidence on the role of Lys41 in catalysis. Furthermore,
insights are given into the structural effects related to the pH-dependent
binding of a sulfate anion, which mimics the phosphate group of RNA, in the
active site. Finally, the results support a number of thermodynamic and kinetic
experimental data concerning the role of the disulfide bridge between Cys65 and
Cys72 in the folding of RNase A.
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Figure 3.
Figure 3 Conformational changes of the catalytic Gln11 and
Lys41. (a) Superposition of the two structures at pH* 5.2 (dark
grey) and 8.0 (light grey); only the most populated conformers
are shown for clarity. (b) Electron-density maps (3F[o] - 2F[c])
contoured at 1.7  for
the structures at pH* 5.2 and (c) at pH* 8.8. The figures were
generated using the program BOBSCRIPT (Esnouf, 1999[Esnouf, R.
M. (1999). Acta Cryst. D55, 938-940.]).
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Figure 6.
Figure 6 Electron-density map (3F[o] - 2F[c]), contoured at 2.7
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showing the double conformation of the disulfide bridge [65-72].
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2002,
58,
441-450)
copyright 2002.
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Secondary reference #1
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Title
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Protein titration in the crystal state.
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Authors
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R.Berisio,
V.S.Lamzin,
F.Sica,
K.S.Wilson,
A.Zagari,
L.Mazzarella.
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Ref.
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J Mol Biol, 1999,
292,
845-854.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2. Electron density maps of some representative
side-chains at acidic pH: the semi-sharpened (F[o]1/2E[o]1/2 -
F[o]1/2E[o]1/2) maps, showing the hydrogen atoms, are
represented in cyano and contoured at 1.6 s (s = 0.03 eÅ
-3).
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Figure 3.
Figure 3. Sequence of snapshots showing the deprotonation
of the imidazole ring of the His12 N  epsilon,
Greek 2 atom: the difference (F[o]1/2E[o]1/2 - F[c]^1/2E[c]^1/2)
maps are represented with a pH-scale colour code (from red/acid
to blue/basic) and are contoured at 1.6 s.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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