2hd9: Difference between revisions
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== | ==Crystal structure of PH1033 from Pyrococcus horikoshii OT3== | ||
<StructureSection load='2hd9' size='340' side='right'caption='[[2hd9]], [[Resolution|resolution]] 1.35Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2hd9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HD9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HD9 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.35Å</td></tr> | |||
[ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> | ||
[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hd9 OCA], [https://pdbe.org/2hd9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hd9 RCSB], [https://www.ebi.ac.uk/pdbsum/2hd9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hd9 ProSAT], [https://www.topsan.org/Proteins/RSGI/2hd9 TOPSAN]</span></td></tr> | ||
[ | </table> | ||
[[ | == Function == | ||
[https://www.uniprot.org/uniprot/Y1033_PYRHO Y1033_PYRHO] | |||
== 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/hd/2hd9_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2hd9 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Protein crystallization is still a major bottleneck in structural biology. As the current methodology of protein crystallization is a type of screening, it is usually difficult to crystallize important target proteins. It was thought that hetero-epitaxic growth from the surface of a mineral crystal acting as a nucleant would be an effective enhancer of protein crystallization. However, in spite of almost two decades of effort, a generally applicable hetero-epitaxic nucleant for protein crystallization has yet to be found. Here we introduce the first candidate for a universal hetero-epitaxic nucleant, microporous zeolite: a synthetic aluminosilicate crystalline polymer with regular micropores. It promotes a form-selective crystal nucleation of proteins and acts as a crystallization catalyst. The most successful zeolite nucleant was molecular sieve type 5A with a pore size of 5 A and with bound Ca2+ ions. The zeolite-mediated crystallization improved the crystal quality in five out of six proteins tested. It provided new crystal forms with better resolution in two cases, larger crystals in one case, and zeolite-dependent crystal formations in two cases. The hetero-epitaxic growth of the zeolite-mediated crystals was confirmed by a crystal-packing analysis which revealed a layer-like structure in the crystal lattice. | |||
Nucleant-mediated protein crystallization with the application of microporous synthetic zeolites.,Sugahara M, Asada Y, Morikawa Y, Kageyama Y, Kunishima N Acta Crystallogr D Biol Crystallogr. 2008 Jun;64(Pt 6):686-95. Epub 2008, May 14. PMID:18560157<ref>PMID:18560157</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2hd9" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Pyrococcus horikoshii OT3]] | |||
[[Category: Kunishima N]] | |||
[[Category: Sugahara M]] | |||
Latest revision as of 11:51, 25 October 2023
Crystal structure of PH1033 from Pyrococcus horikoshii OT3Crystal structure of PH1033 from Pyrococcus horikoshii OT3
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedProtein crystallization is still a major bottleneck in structural biology. As the current methodology of protein crystallization is a type of screening, it is usually difficult to crystallize important target proteins. It was thought that hetero-epitaxic growth from the surface of a mineral crystal acting as a nucleant would be an effective enhancer of protein crystallization. However, in spite of almost two decades of effort, a generally applicable hetero-epitaxic nucleant for protein crystallization has yet to be found. Here we introduce the first candidate for a universal hetero-epitaxic nucleant, microporous zeolite: a synthetic aluminosilicate crystalline polymer with regular micropores. It promotes a form-selective crystal nucleation of proteins and acts as a crystallization catalyst. The most successful zeolite nucleant was molecular sieve type 5A with a pore size of 5 A and with bound Ca2+ ions. The zeolite-mediated crystallization improved the crystal quality in five out of six proteins tested. It provided new crystal forms with better resolution in two cases, larger crystals in one case, and zeolite-dependent crystal formations in two cases. The hetero-epitaxic growth of the zeolite-mediated crystals was confirmed by a crystal-packing analysis which revealed a layer-like structure in the crystal lattice. Nucleant-mediated protein crystallization with the application of microporous synthetic zeolites.,Sugahara M, Asada Y, Morikawa Y, Kageyama Y, Kunishima N Acta Crystallogr D Biol Crystallogr. 2008 Jun;64(Pt 6):686-95. Epub 2008, May 14. PMID:18560157[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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