1okj: Difference between revisions

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{{Seed}}
[[Image:1okj.png|left|200px]]


<!--
==crystal structure of the essential E. coli YeaZ protein by MAD method using the gadolinium complex "DOTMA"==
The line below this paragraph, containing "STRUCTURE_1okj", creates the "Structure Box" on the page.
<StructureSection load='1okj' size='340' side='right'caption='[[1okj]], [[Resolution|resolution]] 2.28&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1okj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OKJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OKJ FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.28&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GD3:GADOLINIUM+ION'>GD3</scene></td></tr>
{{STRUCTURE_1okj|  PDB=1okj  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1okj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1okj OCA], [https://pdbe.org/1okj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1okj RCSB], [https://www.ebi.ac.uk/pdbsum/1okj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1okj ProSAT], [https://www.topsan.org/Proteins/BIGS/1okj TOPSAN]</span></td></tr>
</table>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ok/1okj_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1okj ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A set of seven caged gadolinium complexes were used as vectors for introducing the chelated Gd(3+) ion into protein crystals in order to provide strong anomalous scattering for de novo phasing. The complexes contained multidentate ligand molecules with different functional groups to provide a panel of possible interactions with the protein. An exhaustive crystallographic analysis showed them to be nondisruptive to the diffraction quality of the prepared derivative crystals, and as many as 50% of the derivatives allowed the determination of accurate phases, leading to high-quality experimental electron-density maps. At least two successful derivatives were identified for all tested proteins. Structure refinement showed that the complexes bind to the protein surface or solvent-accessible cavities, involving hydrogen bonds, electrostatic and CH-pi interactions, explaining their versatile binding modes. Their high phasing power, complementary binding modes and ease of use make them highly suitable as a heavy-atom screen for high-throughput de novo structure determination, in combination with the SAD method. They can also provide a reliable tool for the development of new methods such as serial femtosecond crystallography.


===CRYSTAL STRUCTURE OF THE ESSENTIAL E. COLI YEAZ PROTEIN BY MAD METHOD USING THE GADOLINIUM COMPLEX "DOTMA"===
A complement to the modern crystallographer's toolbox: caged gadolinium complexes with versatile binding modes.,Stelter M, Molina R, Jeudy S, Kahn R, Abergel C, Hermoso JA Acta Crystallogr D Biol Crystallogr. 2014 Jun;70(Pt 6):1506-16. doi:, 10.1107/S1399004714005483. Epub 2014 May 23. PMID:24914962<ref>PMID:24914962</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==About this Structure==
</div>
1OKJ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OKJ OCA].
<div class="pdbe-citations 1okj" style="background-color:#fffaf0;"></div>
[[Category: Escherichia coli]]
== References ==
[[Category: Single protein]]
<references/>
[[Category: Abergel, C.]]
__TOC__
[[Category: Claverie, J M.]]
</StructureSection>
[[Category: IGS-CNRS, France BIGSBacterial targets at.]]
[[Category: Escherichia coli K-12]]
[[Category: Jeudy, S.]]
[[Category: Large Structures]]
[[Category: Bacterial targets at igs-cnr]]
[[Category: Abergel C]]
[[Category: Big]]
[[Category: Claverie JM]]
[[Category: France]]
[[Category: Jeudy S]]
[[Category: Hydrolase]]
[[Category: Hypothetical protease yeaz]]
[[Category: Metalloprotease]]
[[Category: Potential zinc protease]]
[[Category: Structural genomic]]
 
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Retrieved from "https://proteopedia.org/1okj"