2q53: Difference between revisions

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[[Image:2q53.~~gif~~|left|200px]]<br />

[[Image:2q53.jpg|left|200px]]<br /><applet load="2q53" size="350" color="white" frame="true" align="right" spinBox="true"

<applet load="2q53" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

caption="2q53, resolution 2.010Å" />

'''Ensemble refinement of the crystal structure of uncharacterized protein loc79017 from Homo sapiens'''<br />

~~==Overview==~~

X-ray crystallography typically uses a single set of coordinates and B, factors to describe macromolecular conformations. Refinement of multiple, copies of the entire structure has been previously used in specific cases, as an alternative means of representing structural flexibility. Here, we, systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of, the distributions of atomic positions in the simulated structures than, single-conformer refinements. Comparison of principal components, calculated from the refined ensembles and simulations shows that concerted, motions are captured locally, but that correlations dissipate over long, distances. Ensemble refinement is also used on 50 experimental structures, of varying resolution and leads to decreases in R(free) values, implying, that improvements in the representation of flexibility observed for the, simulated structures may apply to real structures. These gains are, essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from, ensemble refinement.

==About this Structure==

2Q53 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=2Q53 OCA].

2Q53 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q53 OCA].

==Reference==

~~Ensemble refinement~~ of protein ~~crystal structures: validation and application~~., ~~Levin EJ~~, ~~Kondrashov DA~~, ~~Wesenberg GE~~, Phillips GN Jr, ~~Structure~~. ~~2007 Sep~~;15(9):~~1040~~-52. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=~~17850744 17850744~~]

Crystal structure of Homo sapiens protein LOC79017., Bae E, Bingman CA, Aceti DJ, Phillips GN Jr, Proteins. 2008 Feb 1;70(2):588-91. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17932939 17932939]

[[Category: Homo sapiens]]

[[Category: Single protein]]

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[[Category: unknown function]]

''Page seeded by [http://~~ispc~~.weizmann.ac.il/oca OCA ] on ~~Mon Nov 12~~ 23:29:~~43 2007~~''

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 10:43:25 2008''

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@@ Line 1: / Line 1: @@
-[[Image:2q53.gif|left|200px]]<br />
+[[Image:2q53.jpg|left|200px]]<br /><applet load="2q53" size="350" color="white" frame="true" align="right" spinBox="true"
-<applet load="2q53" size="450" color="white" frame="true" align="right" spinBox="true"
 caption="2q53, resolution 2.010&Aring;" />
 '''Ensemble refinement of the crystal structure of uncharacterized protein loc79017 from Homo sapiens'''<br />
-==Overview==
-X-ray crystallography typically uses a single set of coordinates and B, factors to describe macromolecular conformations. Refinement of multiple, copies of the entire structure has been previously used in specific cases, as an alternative means of representing structural flexibility. Here, we, systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of, the distributions of atomic positions in the simulated structures than, single-conformer refinements. Comparison of principal components, calculated from the refined ensembles and simulations shows that concerted, motions are captured locally, but that correlations dissipate over long, distances. Ensemble refinement is also used on 50 experimental structures, of varying resolution and leads to decreases in R(free) values, implying, that improvements in the representation of flexibility observed for the, simulated structures may apply to real structures. These gains are, essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from, ensemble refinement.
 ==About this Structure==
-Q53 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2Q53 OCA].
+Q53 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q53 OCA].
 ==Reference==
-Ensemble refinement of protein crystal structures: validation and application., Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr, Structure. 2007 Sep;15(9):1040-52. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17850744 17850744]
+Crystal structure of Homo sapiens protein LOC79017., Bae E, Bingman CA, Aceti DJ, Phillips GN Jr, Proteins. 2008 Feb 1;70(2):588-91. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17932939 17932939]
 [[Category: Homo sapiens]]
 [[Category: Single protein]]
@@ Line 28: / Line 24: @@
 [[Category: unknown function]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 23:29:43 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 10:43:25 2008''