5zi9 - Revision history

OCA at 08:56, 22 November 2023

OCA — Wed, 22 Nov 2023 08:56:44 GMT

←Older revision		Revision as of 08:56, 22 November 2023
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	<StructureSection load='5zi9' size='340' side='right'caption='[[5zi9]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5zi9' size='340' side='right'caption='[[5zi9]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zi9]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Strco Strco~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZI9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ZI9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zi9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_coelicolor_A3(2) Streptomyces coelicolor A3(2)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZI9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZI9 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=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.5Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SCO5140 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=100226 STRCO])~~</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=FLC:CITRATE+ANION'>FLC</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'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5zi9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zi9 OCA], [~~http~~://pdbe.org/5zi9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zi9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zi9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zi9 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=5zi9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zi9 OCA], [https://pdbe.org/5zi9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zi9 RCSB], [https://www.ebi.ac.uk/pdbsum/5zi9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zi9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9FBL8_STRCO Q9FBL8_STRCO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Strco]]~~	+	[[Category: Kim K-J]]
-	[[Category: Kim, K J]]	+	[[Category: Seo H]]
-	[[Category: Seo, H]]	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 10:00, 16 September 2020

OCA — Wed, 16 Sep 2020 10:00:59 GMT

←Older revision		Revision as of 10:00, 16 September 2020
Line 1:		Line 1:

-	==Crystal ~~strcuture~~ of type-II LOG from Streptomyces coelicolor A3==	+	==Crystal structure of type-II LOG from Streptomyces coelicolor A3==
-	<StructureSection load='5zi9' size='340' side='right' caption='[[5zi9]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5zi9' size='340' side='right'caption='[[5zi9]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zi9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Strco Strco]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZI9 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZI9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zi9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Strco Strco]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZI9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZI9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SCO5140 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=100226 STRCO])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SCO5140 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=100226 STRCO])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5zi9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zi9 OCA], [http://pdbe.org/5zi9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zi9 RCSB], [http://www.ebi.ac.uk/pdbsum/5zi9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zi9 ProSAT]</span></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=5zi9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zi9 OCA], [http://pdbe.org/5zi9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zi9 RCSB], [http://www.ebi.ac.uk/pdbsum/5zi9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zi9 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Strco]]		[[Category: Strco]]
	[[Category: Kim, K J]]		[[Category: Kim, K J]]
	[[Category: Seo, H]]		[[Category: Seo, H]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 08:29, 2 May 2018

OCA — Wed, 02 May 2018 08:29:10 GMT

←Older revision		Revision as of 08:29, 2 May 2018
Line 3:		Line 3:
	<StructureSection load='5zi9' size='340' side='right' caption='[[5zi9]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5zi9' size='340' side='right' caption='[[5zi9]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zi9]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZI9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZI9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zi9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Strco Strco]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZI9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZI9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SCO5140 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=100226 STRCO])</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5zi9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zi9 OCA], [http://pdbe.org/5zi9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zi9 RCSB], [http://www.ebi.ac.uk/pdbsum/5zi9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zi9 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5zi9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zi9 OCA], [http://pdbe.org/5zi9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zi9 RCSB], [http://www.ebi.ac.uk/pdbsum/5zi9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zi9 ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Strco]]
	[[Category: Kim, K J]]		[[Category: Kim, K J]]
	[[Category: Seo, H]]		[[Category: Seo, H]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 05:43, 18 April 2018

OCA — Wed, 18 Apr 2018 05:43:02 GMT

←Older revision		Revision as of 05:43, 18 April 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zi9 is ~~ON HOLD until Paper~~ Publication	+	==Crystal strcuture of type-II LOG from Streptomyces coelicolor A3==
		+	<StructureSection load='5zi9' size='340' side='right' caption='[[5zi9]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zi9]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZI9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZI9 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5zi9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zi9 OCA], [http://pdbe.org/5zi9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zi9 RCSB], [http://www.ebi.ac.uk/pdbsum/5zi9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zi9 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Streptomyces coelicolor A3 contains Sc5140, a gene coding for poorly understood bacterial LOG-like protein. In this study, we determined the crystal structure of Sc5140 and found it resembles the overall structure of other type-II LOGs. In addition, Sc5140 exhibited phosphoribohydrolase activity against adenosine monophosphate (AMP), indicating that it had the same function as known type-II LOGs. Based on these results, we designated Sc5140 as ScLOGII. We performed docking calculations of AMP into the ScLOGII structure, which suggested the mode of binding for type-II LOG with their AMP substrate. The ScLOGII structure uniquely exhibited a long tail-like structure at the N-terminus that was involved in hexamerization of the protein; the disordered N-terminal region (DNR). Truncation of DNR in ScLOGII negatively affected both the phosphoribohydrolase activity and the oligomerization of the protein, suggesting that this region functioned in enzyme stabilization. However, results from truncation experiments using ScLOGII and CgLOGII, a type-II LOG homologue from Corynebacterium glutamicum, were quite different, leaving uncertainty regarding the general functions of DNR in type-II LOGs. Overall, the current structural work may help in understand the significance of type-II LOG protein at the molecular level.

-	~~Authors: Seo~~, H., Kim~~, K~~.-J.	+	Structural and biochemical characterization of the type-II LOG protein from Streptomyces coelicolor A3.,Seo H, Kim KJ Biochem Biophys Res Commun. 2018 May 15;499(3):577-583. doi:, 10.1016/j.bbrc.2018.03.193. Epub 2018 Mar 30. PMID:29596827<ref>PMID:29596827</ref>

-	~~Description: Crystal strcuture~~ of ~~type-II LOG from Streptomyces coelicolor A3~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: Kim, K.-J]]	+	<div class="pdbe-citations 5zi9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kim, K J]]
	[[Category: Seo, H]]		[[Category: Seo, H]]
		+	[[Category: Hydrolase]]

OCA at 12:17, 11 April 2018

OCA — Wed, 11 Apr 2018 12:17:45 GMT

←Older revision		Revision as of 12:17, 11 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zi9 is ON HOLD	+	The entry 5zi9 is ON HOLD until Paper Publication

	Authors: Seo, H., Kim, K.-J.		Authors: Seo, H., Kim, K.-J.

OCA: Protected "5zi9" [edit=sysop:move=sysop]

OCA — Wed, 21 Mar 2018 06:02:48 GMT

Protected "5zi9" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:02, 21 March 2018

OCA: New page: '''Unreleased structure''' The entry 5zi9 is ON HOLD Authors: Seo, H., Kim, K.-J. Description: Crystal strcuture of type-II LOG from Streptomyces coelicolor A3 [[Category: Unreleased S...

OCA — Wed, 21 Mar 2018 06:02:47 GMT

New page: '''Unreleased structure''' The entry 5zi9 is ON HOLD Authors: Seo, H., Kim, K.-J. Description: Crystal strcuture of type-II LOG from Streptomyces coelicolor A3 [[Category: Unreleased S...

New page

'''Unreleased structure'''

The entry 5zi9 is ON HOLD

Authors: Seo, H., Kim, K.-J.

Description: Crystal strcuture of type-II LOG from Streptomyces coelicolor A3
[[Category: Unreleased Structures]]
[[Category: Kim, K.-J]]
[[Category: Seo, H]]