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PDBsum entry 1jiy
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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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The effect of stabilizing additives on the structure and hydration of proteins: a study involving tetragonal lysozyme.
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Authors
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S.Datta,
B.K.Biswal,
M.Vijayan.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2001,
57,
1614-1620.
[DOI no: ]
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PubMed id
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Abstract
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In order to elucidate the effect of stabilizing additives on the structure of
proteins and the associated ordered water molecules in the hydration shell, the
crystal structures of tetragonal lysozyme grown in the presence of sucrose,
sorbitol and trehalose have been refined. Also refined are the structures of
orthorhombic and monoclinic lysozyme grown under the conditions in which
tetragonal lysozyme is normally grown. A comparison of the two sets of
structures with the structure of native tetragonal lysozyme shows that the
effect of the additives on the structure of the protein molecule is less than
that of the normal minor changes associated with differences in molecular
packing. Surprisingly, the same is true of the effect on the hydration shell,
represented by the ordered water molecules attached to the protein. Thus, it
appears that the cause of the stabilizing effect of the additives needs to be
sought outside the immediate neighbourhood of the protein molecule. Sorbitol and
trehalose do not coherently interact with the protein. One sucrose molecule
binds at the active-site cleft of the enzyme.
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Figure 3.
Figure 3 Schematic representation of the interactions of sucrose
with the enzyme molecule. This figure was prepared using LIGPLOT
(Wallace et al., 1995[Wallace, A. C., Laskowski, R. A. &
Thornton, J. M. (1995). Protein Eng. 8, 127-134.]).
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The above figure is
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2001,
57,
1614-1620)
copyright 2001.
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Secondary reference #1
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Title
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Hydration, Mobility and accessibility of lysozyme: structures of a ph 6.5 orthorhombic form and its low-Humidity variant and a comparative study involving 20 crystallographically independent molecules.
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Authors
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B.K.Biswal,
N.Sukumar,
M.Vijayan.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2000,
56,
1110-1119.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1 Deviations of C^  positions
between native pH 9.5 and pH 4.5 forms (cyan), pH 9.5 and pH 6.5
forms (magenta) and pH 6.5 and pH 4.5 forms (blue).
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Figure 2.
Figure 2 Deviations of C^ positions
between the native and low-humidity variant of the pH 9.5 form
(red) and the pH 6.5 form (green).
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The above figures are
reproduced from the cited reference
with permission from the IUCr
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Secondary reference #2
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Title
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Protein hydration and water structure: X-Ray analysis of a closely packed protein crystal with very low solvent content.
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Authors
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Madhusudan,
R.Kodandapani,
M.Vijayan.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1993,
49,
234-245.
[DOI no: ]
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PubMed id
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Figure 10.
Fig. 10. (a), () Interctions involving the two nitrate ions. Figures
in parentheses refer to the molecular numbering (Fig. 9).
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Figure 11.
Fig. 11. The largest water cluster in the structure involving 42
water molecules.
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The above figures are
reproduced from the cited reference
with permission from the IUCr
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