2q4x

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[[Image:2q4x.png|left|200px]]
 
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==Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g16990==
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The line below this paragraph, containing "STRUCTURE_2q4x", creates the "Structure Box" on the page.
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<StructureSection load='2q4x' size='340' side='right'caption='[[2q4x]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2q4x]] is a 2 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=2Q4X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4X FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.1&#8491;, 8 models</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=HMH:4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE'>HMH</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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{{STRUCTURE_2q4x| PDB=2q4x | SCENE= }}
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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=2q4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4x OCA], [https://pdbe.org/2q4x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4x RCSB], [https://www.ebi.ac.uk/pdbsum/2q4x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4x ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/TENAE_ARATH TENAE_ARATH] Involved in thiamine salvage by hydrolyzing the thiamine breakdown product 4-amino-5-aminomethyl-2-methylpyrimidine (amino-HMP) to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) (PubMed:25014715). Has a high formylamino-HMP amidohydrolase activity (PubMed:25014715). No activity with other thiamine degradation products such as thiamine mono- or diphosphate, oxothiamine, oxythiamine, thiamine disulfide, desthiothiamine or thiochrome as substrates (PubMed:25014715). Does not display thiaminase II activity, as it is unable to hydrolyze thiamine (PubMed:25014715). Is able to carry out two successive steps in the salvage of thiamine breakdown product, whereas two separate enzymes are required in Bacillus species (Probable). May also serve a damage pre-emption function by hydrolyzing products that would otherwise do harm (Probable).<ref>PMID:25014715</ref> <ref>PMID:25014715</ref>
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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/q4/2q4x_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2q4x 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 gene product from Arabidopsis thaliana At3g16990===
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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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The line below this paragraph, {{ABSTRACT_PUBMED_17850744}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2q4x" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 17850744 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_17850744}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[2q4x]] is a 2 chain structure with 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=2Q4X OCA].
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==Reference==
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<ref group="xtra">PMID:017850744</ref><ref group="xtra">PMID:015326608</ref><references group="xtra"/>
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[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
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[[Category: CESG, Center for Eukaryotic Structural Genomics.]]
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[[Category: Large Structures]]
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[[Category: Kondrashov, D A.]]
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[[Category: Kondrashov DA]]
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[[Category: Levin, E J.]]
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[[Category: Levin EJ]]
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[[Category: Phillips, G N.]]
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[[Category: Phillips Jr GN]]
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[[Category: Wesenberg, G E.]]
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[[Category: Wesenberg GE]]
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[[Category: At3g16990]]
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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: Plant protein]]
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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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[[Category: Tena/thi-4/pqqc family]]
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[[Category: Tena_thi-4 domain]]
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Current revision

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g16990

PDB ID 2q4x

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