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PDBsum entry 1x6r
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Structural protein
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PDB id
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1x6r
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References listed in PDB file
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Key reference
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Title
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Pros and cons of cryocrystallography: should we also collect a room-Temperature data set?
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Authors
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K.V.Dunlop,
R.T.Irvin,
B.Hazes.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2005,
61,
80-87.
[DOI no: ]
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PubMed id
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Abstract
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High-resolution protein structures are becoming more common owing to the
availability of increasingly brilliant synchrotron X-ray sources. However, to
withstand the increased X-ray dose the crystals must be held at cryogenic
temperatures. To compare the benefit of increased resolution with the drawback
of potential temperature-induced changes, three room-temperature and three
cryogenic data sets for PAK pilin have been collected at resolutions between 1.8
and 0.78 A. The results show that although the high-resolution cryogenic
structures are more precise and more detailed, they also show systematic
deviations from the room-temperature structures. Small but significant
differences are even observed in the structural core, whilst more extensive
changes occur at the protein surface. These differences can affect biological
interpretations, especially because many important biological processes take
place at the protein surface. Accordingly, although high-quality cryogenic
synchrotron data is extremely valuable to protein crystallography,
room-temperature structures are still desirable, especially if the research
question involves protein features that are sensitive to temperature-induced
changes.
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Figure 3.
Figure 3 2F[o] - F[c] density for Glu27 contoured at 1  .
Density for structure 3 (yellow) shows two Glu27 side-chain
conformations. Density for structure 4 (green) shows only one
side-chain conformation. Structures 3 and 4 are representative
of all cryocooled and all room-temperature structures,
respectively. The figure was produced using Xfit (McRee,
1999[McRee, D. E. (1999). J. Struct. Biol. 125, 156-165.]) and
Raster3D (Merritt & Murphy, 1994[Merritt, E. A. & Murphy, M. E.
P. (1994). Acta Cryst. D50, 869-873.]).
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Figure 4.
Figure 4 Ball-and-stick model showing superimposed cryocooled
(green) and room-temperature (dark blue) water molecules for all
six PAK structures within a small section of the PAK protein.
The structure shows that waters observed in room-temperature
structures are also present in cryocooled structures but not
vice versa. The figure was made using Xfit (McRee, 1999[McRee,
D. E. (1999). J. Struct. Biol. 125, 156-165.]) and Raster3D
(Merritt & Murphy, 1994[Merritt, E. A. & Murphy, M. E. P.
(1994). Acta Cryst. D50, 869-873.]).
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2005,
61,
80-87)
copyright 2005.
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