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2q4w

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(New page: 200px<br /><applet load="2q4w" size="450" color="white" frame="true" align="right" spinBox="true" caption="2q4w, resolution 1.700&Aring;" /> '''Ensemble refinement...)
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[[Image:2q4w.jpg|left|200px]]<br /><applet load="2q4w" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2q4w, resolution 1.700&Aring;" />
 
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'''Ensemble refinement of the protein crystal structure of cytokinin oxidase/dehydrogenase (CKX) from Arabidopsis thaliana At5g21482'''<br />
 
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==Overview==
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==Ensemble refinement of the protein crystal structure of cytokinin oxidase/dehydrogenase (CKX) from Arabidopsis thaliana At5g21482==
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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.
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<StructureSection load='2q4w' size='340' side='right'caption='[[2q4w]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2q4w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4W FirstGlance]. <br>
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2Q4W 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 FAD as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Cytokinin_dehydrogenase Cytokinin dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.99.12 1.5.99.12] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2Q4W OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4w OCA], [https://pdbe.org/2q4w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4w RCSB], [https://www.ebi.ac.uk/pdbsum/2q4w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4w ProSAT]</span></td></tr>
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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]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/CKX7_ARATH CKX7_ARATH] Catalyzes the oxidation of cytokinins, a family of N(6)-substituted adenine derivatives that are plant hormones, where the substituent is an isopentenyl group (By similarity).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q4/2q4w_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2q4w ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
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[[Category: Cytokinin dehydrogenase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Kondrashov DA]]
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[[Category: CESG, Center.for.Eukaryotic.Structural.Genomics.]]
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[[Category: Levin EJ]]
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[[Category: Jr., G.N.Phillips.]]
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[[Category: Phillips Jr GN]]
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[[Category: Kondrashov, D.A.]]
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[[Category: Wesenberg GE]]
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[[Category: Levin, E.J.]]
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[[Category: Wesenberg, G.E.]]
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[[Category: FAD]]
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[[Category: at5g21482.1]]
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[[Category: center for eukaryotic structural genomics]]
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[[Category: cesg]]
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[[Category: ckx]]
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[[Category: cytokinin oxidase/dehydrogenase]]
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[[Category: ensemble refinement]]
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[[Category: oxidoreductase]]
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[[Category: protein structure initiative]]
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[[Category: psi]]
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[[Category: refinement methodology development]]
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[[Category: structural genomics]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 13:48:58 2007''
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Current revision

Ensemble refinement of the protein crystal structure of cytokinin oxidase/dehydrogenase (CKX) from Arabidopsis thaliana At5g21482

PDB ID 2q4w

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