2q41

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[[Image:2q41.jpg|left|200px]]
 
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{{Structure
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==Ensemble refinement of the protein crystal structure of spermidine synthase from Arabidopsis thaliana gene At1g23820==
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|PDB= 2q41 |SIZE=350|CAPTION= <scene name='initialview01'>2q41</scene>, resolution 2.700&Aring;
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<StructureSection load='2q41' size='340' side='right'caption='[[2q41]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>
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<table><tr><td colspan='2'>[[2q41]] is a 4 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=2Q41 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q41 FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Spermidine_synthase Spermidine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.16 2.5.1.16] </span>
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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]] 2.7&#8491;</td></tr>
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|GENE= SPDSYN1, At1g23820, F5O8.38 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam01564 Spermine_synth]</span>
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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=2q41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q41 OCA], [https://pdbe.org/2q41 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q41 RCSB], [https://www.ebi.ac.uk/pdbsum/2q41 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q41 ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1xj5|1XJ5]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q41 OCA], [http://www.ebi.ac.uk/pdbsum/2q41 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2q41 RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/SPDS1_ARATH SPDS1_ARATH]
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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/q4/2q41_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=2q41 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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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'''Ensemble refinement of the protein crystal structure of spermidine synthase from Arabidopsis thaliana gene At1g23820'''
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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:17850744<ref>PMID:17850744</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2q41" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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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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*[[Spermidine synthase 3D structures|Spermidine synthase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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2Q41 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=2Q41 OCA].
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__TOC__
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</StructureSection>
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==Reference==
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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://www.ncbi.nlm.nih.gov/pubmed/17850744 17850744]
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[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Spermidine synthase]]
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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: at1g23820]]
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[[Category: center for eukaryotic structural genomic]]
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[[Category: cesg]]
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[[Category: ensemble refinement]]
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[[Category: polyamine]]
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[[Category: protein structure initiative]]
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[[Category: psi]]
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[[Category: putrescine aminopropyl transferase]]
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[[Category: refinement methodology development]]
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[[Category: spds1]]
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[[Category: spermidine synthase]]
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[[Category: structural genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:44:21 2008''
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Current revision

Ensemble refinement of the protein crystal structure of spermidine synthase from Arabidopsis thaliana gene At1g23820

PDB ID 2q41

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