6ztx - Revision history

OCA at 11:58, 1 February 2024

OCA — Thu, 01 Feb 2024 11:58:19 GMT

←Older revision		Revision as of 11:58, 1 February 2024
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	<StructureSection load='6ztx' size='340' side='right'caption='[[6ztx]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='6ztx' size='340' side='right'caption='[[6ztx]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ztx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Escherichia_coli_k12~~ Escherichia coli ~~k12~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZTX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZTX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ztx]] 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=6ZTX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZTX FirstGlance]. <br>
-	</td></tr><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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HDD:CIS-HEME+D+HYDROXYCHLORIN+GAMMA-SPIROLACTONE'>HDD</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.3Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Catalase Catalase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </span></td></tr>	+	<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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HDD:CIS-HEME+D+HYDROXYCHLORIN+GAMMA-SPIROLACTONE'>HDD</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=6ztx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ztx OCA], [https://pdbe.org/6ztx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ztx RCSB], [https://www.ebi.ac.uk/pdbsum/6ztx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ztx ProSAT]</span></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=6ztx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ztx OCA], [https://pdbe.org/6ztx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ztx RCSB], [https://www.ebi.ac.uk/pdbsum/6ztx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ztx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CATE_ECOLI CATE_ECOLI]] Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.	+	[https://www.uniprot.org/uniprot/CATE_ECOLI CATE_ECOLI] Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	~~[[Category: Catalase]]~~	+	[[Category: Escherichia coli K-12]]
-	[[Category: Escherichia coli ~~k12~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Grzechowiak, M]]	+	[[Category: Grzechowiak M]]
-	[[Category: Ruszkowski, M]]	+	[[Category: Ruszkowski M]]
-	[[Category: Sekula, B]]	+	[[Category: Sekula B]]
-	~~[[Category: Artifact crystallization]]~~	+
-	~~[[Category: Contamination]]~~	+
-	~~[[Category: Heme]]~~	+
-	~~[[Category: Hydrogen-peroxide]]~~	+
-	~~[[Category: Impurity]]~~	+
-	~~[[Category: Iron]]~~	+
-	~~[[Category: Oxidative stress]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 15:00, 3 March 2021

OCA — Wed, 03 Mar 2021 15:00:07 GMT

←Older revision		Revision as of 15:00, 3 March 2021
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	==Crystal Structure of catalase HPII from Escherichia coli (serendipitously crystallized)==		==Crystal Structure of catalase HPII from Escherichia coli (serendipitously crystallized)==
-	<StructureSection load='6ztx' size='340' side='right'caption='[[6ztx]]' scene=''>	+	<StructureSection load='6ztx' size='340' side='right'caption='[[6ztx]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZTX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZTX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ztx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZTX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZTX FirstGlance]. <br>
-	</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=6ztx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ztx OCA], [https://pdbe.org/6ztx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ztx RCSB], [https://www.ebi.ac.uk/pdbsum/6ztx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ztx ProSAT]</span></td></tr>	+	</td></tr><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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HDD:CIS-HEME+D+HYDROXYCHLORIN+GAMMA-SPIROLACTONE'>HDD</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Catalase Catalase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </span></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=6ztx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ztx OCA], [https://pdbe.org/6ztx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ztx RCSB], [https://www.ebi.ac.uk/pdbsum/6ztx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ztx ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/CATE_ECOLI CATE_ECOLI]] Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protein crystallographers are well aware of the trap of crystallizing E. coli proteins instead of the macromolecule of interest if heterologous recombinant protein expression in E. coli was part of the experimental pipeline. Among the well-known culprits are YodA metal-binding lipocalin (25 kDa) and YadF carbonic anhydrase (a tetramer of 25 kDa subunits). We report a novel crystal form of another such culprit, E. coli HPII catalase, which is a tetrameric protein of ~340 kDa molecular weight. HPII is likely to contaminate recombinant protein samples, co-purify, and then co-crystallize with the target proteins, especially if their masses in size exclusion chromatography are ~300-400 kDa. What makes this case more interesting but also parlous, is the fact that HPII can crystallize from very low concentrations, even well below 1 mg/mL.
		+
		+	Serendipitous crystallization of E. coli HPII catalase, a sequel to "the tale usually not told".,Grzechowiak M, Sekula B, Jaskolski M, Ruszkowski M Acta Biochim Pol. 2021 Jan 24. pii: 5501. doi: 10.18388/abp.2020_5501. PMID:33485289<ref>PMID:33485289</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ztx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Catalase]]
		+	[[Category: Escherichia coli k12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Grzechowiak M]]	+	[[Category: Grzechowiak, M]]
-	[[Category: Ruszkowski M]]	+	[[Category: Ruszkowski, M]]
-	[[Category: Sekula B]]	+	[[Category: Sekula, B]]
		+	[[Category: Artifact crystallization]]
		+	[[Category: Contamination]]
		+	[[Category: Heme]]
		+	[[Category: Hydrogen-peroxide]]
		+	[[Category: Impurity]]
		+	[[Category: Iron]]
		+	[[Category: Oxidative stress]]
		+	[[Category: Oxidoreductase]]

OCA at 06:46, 24 February 2021

OCA — Wed, 24 Feb 2021 06:46:35 GMT

←Older revision		Revision as of 06:46, 24 February 2021
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	<StructureSection load='6ztx' size='340' side='right'caption='[[6ztx]]' scene=''>		<StructureSection load='6ztx' size='340' side='right'caption='[[6ztx]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZTX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6ZTX FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZTX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZTX FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6ztx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ztx OCA], [~~http~~://pdbe.org/6ztx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ztx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ztx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ztx ProSAT]</span></td></tr>	+	</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=6ztx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ztx OCA], [https://pdbe.org/6ztx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ztx RCSB], [https://www.ebi.ac.uk/pdbsum/6ztx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ztx ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 06:22, 7 October 2020

OCA — Wed, 07 Oct 2020 06:22:00 GMT

←Older revision		Revision as of 06:22, 7 October 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ztx ~~is ON HOLD~~	+	==Crystal Structure of catalase HPII from Escherichia coli (serendipitously crystallized)==
-		+	<StructureSection load='6ztx' size='340' side='right'caption='[[6ztx]]' scene=''>
-	~~Authors~~: ~~Grzechowiak~~, M., ~~Sekula~~, B., ~~Ruszkowski~~, M.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZTX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZTX FirstGlance]. <br>
-	~~Description: Crystal Structure of catalase HPII from Escherichia coli (serendipitously crystallized)~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6ztx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ztx OCA], [http://pdbe.org/6ztx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ztx RCSB], [http://www.ebi.ac.uk/pdbsum/6ztx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ztx ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Sekula, B~~]]	+	__TOC__
-	[[Category: Ruszkowski, M]]	+	</StructureSection>
-	[[Category: ~~Grzechowiak, M~~]]	+	[[Category: Large Structures]]
		+	[[Category: Grzechowiak M]]
		+	[[Category: Ruszkowski M]]
		+	[[Category: Sekula B]]

OCA: Protected "6ztx" [edit=sysop:move=sysop]

OCA — Wed, 29 Jul 2020 09:35:11 GMT

Protected "6ztx" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:35, 29 July 2020

OCA: New page: '''Unreleased structure''' The entry 6ztx is ON HOLD Authors: Grzechowiak, M., Sekula, B., Ruszkowski, M. Description: Crystal Structure of catalase HPII from Escherichia coli (serendi...

OCA — Wed, 29 Jul 2020 09:35:10 GMT

New page: '''Unreleased structure''' The entry 6ztx is ON HOLD Authors: Grzechowiak, M., Sekula, B., Ruszkowski, M. Description: Crystal Structure of catalase HPII from Escherichia coli (serendi...

New page

'''Unreleased structure'''

The entry 6ztx is ON HOLD

Authors: Grzechowiak, M., Sekula, B., Ruszkowski, M.

Description: Crystal Structure of catalase HPII from Escherichia coli (serendipitously crystallized)
[[Category: Unreleased Structures]]
[[Category: Sekula, B]]
[[Category: Ruszkowski, M]]
[[Category: Grzechowiak, M]]