2q4d: Difference between revisions

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Revision as of 19:21, 20 March 2008

File:2q4d.jpg

, resolution 2.152Å

Ligands:

and

Gene:

AT5G11950, F14F18.120 (Arabidopsis thaliana)

Coordinates:

save as pdb, mmCIF, xml

Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At5g11950

OverviewOverview

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 StructureAbout this Structure

2Q4D is a Single protein structure of sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA.

ReferenceReference

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:17850744

Page seeded by OCA on Thu Mar 20 18:21:31 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2q4d.jpg|left|200px]]<br /><applet load="2q4d" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:2q4d.jpg|left|200px]]
-caption="2q4d, resolution 2.152&Aring;" />
-'''Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At5g11950'''<br />
+ {{Structure
+|PDB= 2q4d |SIZE=350|CAPTION= <scene name='initialview01'>2q4d</scene>, resolution 2.152&Aring;
+|SITE=
+|LIGAND= <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene> and <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>
+|ACTIVITY=
+|GENE= AT5G11950, F14F18.120 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])
+}}
+'''Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At5g11950'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-Q4D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] with <scene name='pdbligand=NO3:'>NO3</scene> and <scene name='pdbligand=EDO:'>EDO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4D OCA].
+Q4D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4D 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]
+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://www.ncbi.nlm.nih.gov/pubmed/17850744 17850744]
 [[Category: Arabidopsis thaliana]]
 [[Category: Single protein]]
@@ Line 21: / Line 30: @@
 [[Category: NO3]]
 [[Category: at5g11950]]
-[[Category: center for eukaryotic structural genomics]]
+[[Category: center for eukaryotic structural genomic]]
 [[Category: cesg]]
 [[Category: ensemble refinement]]
@@ Line 28: / Line 37: @@
 [[Category: psi]]
 [[Category: refinement methodology development]]
-[[Category: structural genomics]]
+[[Category: structural genomic]]
 [[Category: unknown function]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:35:52 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:21:31 2008''