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PDBsum entry 1dwh
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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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Structural changes in a cryo-Cooled protein crystal owing to radiation damage.
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Author
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W.P.Burmeister.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2000,
56,
328-341.
[DOI no: ]
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PubMed id
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Abstract
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The high intensity of third-generation X-ray sources, along with the development
of cryo-cooling of protein crystals at temperatures around 100 K, have made it
possible to extend the diffraction limit of crystals and to reduce their size.
However, even with cryo-cooled crystals, radiation damage becomes a limiting
factor. So far, the radiation damage has manifested itself in the form of a loss
of overall diffracted intensity and an increase in the temperature factor. The
structure of a protein (myrosinase) after exposure to different doses of X-rays
in the region of 20 x 10(15) photons mm(-2) has been studied. The changes in the
structure owing to radiation damage were analysed using Fourier difference maps
and occupancy refinement for the first time. Damage was obvious in the form of
breakage of disulfide bonds, decarboxylation of aspartate and glutamate
residues, a loss of hydroxyl groups from tyrosine and of the methylthio group of
methionine. The susceptibility to radiation damage of individual groups of the
same kind varies within the protein. The quality of the model resulting from
structure determination might be compromised owing to the presence of radiolysis
in the crystal after an excessive radiation dose. Radiation-induced structural
changes may interfere with the interpretation of ligand-binding studies or MAD
data. The experiments reported here suggest that there is an intrinsic limit to
the amount of data which can be extracted from a sample of a given size.
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Figure 1.
Figure 1 Radical reactions caused by X-ray or electron
irradiation which are likely to contribute to the observed
radiation damage to the amino-acid side chains. (p)- represents
protein. References for the reactions are given in the text. The
mechanism for reaction (5) is not known; only the products have
been identified (Schimazu et al., 1964[Berthet-Colominas, C.,
Monaco, S., Novelli, A., Sibaļ, G., Mallet, F. & Cusack, S.
(1999). EMBO J. 18, 1124-1136.]).
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Figure 5.
Figure 5 Individually refined occupancies of labile groups. The
most rapid loss of electron density (plotted with squares,
residue name given) is fitted with an exponential function
(dotted line). The rate constants obtained from these fits are
given in Table 2-; the scatter of the points gives an idea of
the statistical errors of the refined occupancies. The groups
shown in Fig. 3-are plotted as black squares. (a) S atoms of
free cysteines (dashed lines) and disulfide bridges (solid
lines). (b) Carboxyl groups of glutamic acid residues. (c)
Carboxyl groups of aspartate residues. For clarity, the
connecting lines are only drawn for every fifth residue. Asp70
(triangles) is involved in the coordination of the Zn atom. (d)
Hydroxyl groups of tyrosine. For clarity, the connecting lines
are only drawn for every fifth residue. (e) Methylthio groups of
methionine.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2000,
56,
328-341)
copyright 2000.
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Secondary reference #1
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Title
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The crystal structures of sinapis alba myrosinase and a covalent glycosyl-Enzyme intermediate provide insights into the substrate recognition and active-Site machinery of an s-Glycosidase.
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Authors
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W.P.Burmeister,
S.Cottaz,
H.Driguez,
R.Iori,
S.Palmieri,
B.Henrissat.
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Ref.
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Structure, 1997,
5,
663-675.
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PubMed id
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