2q4s

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[[Image:2q4s.jpg|left|200px]]
 
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{{Structure
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==Ensemble refinement of the protein crystal structure of cysteine dioxygenase type I from Mus musculus Mm.241056==
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|PDB= 2q4s |SIZE=350|CAPTION= <scene name='initialview01'>2q4s</scene>, resolution 1.750&Aring;
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<StructureSection load='2q4s' size='340' side='right'caption='[[2q4s]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>
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<table><tr><td colspan='2'>[[2q4s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4S FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Cysteine_dioxygenase Cysteine dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.20 1.13.11.20] </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]] 1.75&#8491;</td></tr>
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|GENE= Cdo1, Mm.241056 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
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|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam05995 CDO_I]</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=2q4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4s OCA], [https://pdbe.org/2q4s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4s RCSB], [https://www.ebi.ac.uk/pdbsum/2q4s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4s ProSAT]</span></td></tr>
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|RELATEDENTRY=[[2atf|2ATF]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4s OCA], [http://www.ebi.ac.uk/pdbsum/2q4s PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2q4s RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/CDO1_MOUSE CDO1_MOUSE]
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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/q4/2q4s_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=2q4s 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 cysteine dioxygenase type I from Mus musculus Mm.241056'''
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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 2q4s" 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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*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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2Q4S is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4S OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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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: Cysteine dioxygenase]]
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[[Category: Mus musculus]]
[[Category: Mus musculus]]
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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: bc013638]]
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[[Category: center for eukaryotic structural genomic]]
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[[Category: cesg]]
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[[Category: cupin family]]
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[[Category: ensemble refinement]]
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[[Category: mm 241056]]
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[[Category: oxidoreductase]]
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[[Category: pfam05995 2 cdo_i]]
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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 genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:44:44 2008''
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Current revision

Ensemble refinement of the protein crystal structure of cysteine dioxygenase type I from Mus musculus Mm.241056

PDB ID 2q4s

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