5c6m - Revision history

OCA at 11:18, 10 January 2024

OCA — Wed, 10 Jan 2024 11:18:53 GMT

←Older revision		Revision as of 11:18, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5c6m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_halifaxensis Shewanella halifaxensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C6M FirstGlance]. <br>		<table><tr><td colspan='2'>[[5c6m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_halifaxensis Shewanella halifaxensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C6M FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.76Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5c6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c6m OCA], [https://pdbe.org/5c6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c6m RCSB], [https://www.ebi.ac.uk/pdbsum/5c6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c6m 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=5c6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c6m OCA], [https://pdbe.org/5c6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c6m RCSB], [https://www.ebi.ac.uk/pdbsum/5c6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c6m ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:22, 7 June 2023

OCA — Wed, 07 Jun 2023 06:22:06 GMT

←Older revision		Revision as of 06:22, 7 June 2023
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	<StructureSection load='5c6m' size='340' side='right'caption='[[5c6m]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='5c6m' size='340' side='right'caption='[[5c6m]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5c6m]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Dsm_17350 Dsm 17350~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C6M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5C6M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5c6m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_halifaxensis Shewanella halifaxensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C6M FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">deoC, Shal_3136 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271098 DSM 17350])</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=5c6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c6m OCA], [https://pdbe.org/5c6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c6m RCSB], [https://www.ebi.ac.uk/pdbsum/5c6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c6m ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribose-phosphate_aldolase Deoxyribose-phosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.4 4.1.2.4] </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=5c6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c6m OCA], [~~http~~://pdbe.org/5c6m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5c6m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5c6m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5c6m ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DEOC_SHEHH DEOC_SHEHH]] Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.	+	[https://www.uniprot.org/uniprot/DEOC_SHEHH DEOC_SHEHH] Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.
	<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: Deoxyribose-phosphate aldolase]]
-	[[Category: Dsm 17350]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bramski, J~~]]	+	[[Category: Shewanella halifaxensis]]
-	[[Category: ~~Dick, M]]~~	+	[[Category: Bramski J]]
-	~~[[Category: Pietruszka,~~ J]]	+	[[Category: Dick M]]
-	[[Category: ~~Weiergraeber, O H~~]]	+	[[Category: Pietruszka J]]
-	[[Category: ~~Dera~~]]	+	[[Category: Weiergraeber OH]]
-	[[Category: ~~Lyase]]~~	+
-	~~[[Category: Psychrophilic]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 11:14, 18 March 2020

OCA — Wed, 18 Mar 2020 11:14:05 GMT

←Older revision		Revision as of 11:14, 18 March 2020
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		+
	==Crystal structure of deoxyribose-phosphate aldolase from Shewanella halifaxensis==		==Crystal structure of deoxyribose-phosphate aldolase from Shewanella halifaxensis==
-	<StructureSection load='5c6m' size='340' side='right' caption='[[5c6m]], [[Resolution\|resolution]] 1.76Å' scene=''>	+	<StructureSection load='5c6m' size='340' side='right'caption='[[5c6m]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5c6m]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C6M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C6M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5c6m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_17350 Dsm 17350]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C6M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C6M FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">deoC, Shal_3136 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271098 DSM 17350])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribose-phosphate_aldolase Deoxyribose-phosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.4 4.1.2.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribose-phosphate_aldolase Deoxyribose-phosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.4 4.1.2.4] </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=5c6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c6m OCA], [http://pdbe.org/5c6m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c6m RCSB], [http://www.ebi.ac.uk/pdbsum/5c6m PDBsum]</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=5c6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c6m OCA], [http://pdbe.org/5c6m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c6m RCSB], [http://www.ebi.ac.uk/pdbsum/5c6m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5c6m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5c6m" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5c6m" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aldolase 3D structures\|Aldolase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Deoxyribose-phosphate aldolase]]		[[Category: Deoxyribose-phosphate aldolase]]
		+	[[Category: Dsm 17350]]
		+	[[Category: Large Structures]]
	[[Category: Bramski, J]]		[[Category: Bramski, J]]
	[[Category: Dick, M]]		[[Category: Dick, M]]

OCA at 15:45, 3 February 2016

OCA — Wed, 03 Feb 2016 15:45:13 GMT

←Older revision		Revision as of 15:45, 3 February 2016
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of deoxyribose-phosphate aldolase from Shewanella halifaxensis==
		+	<StructureSection load='5c6m' size='340' side='right' caption='[[5c6m]], [[Resolution\|resolution]] 1.76Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5c6m]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C6M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C6M FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribose-phosphate_aldolase Deoxyribose-phosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.4 4.1.2.4] </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=5c6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c6m OCA], [http://pdbe.org/5c6m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c6m RCSB], [http://www.ebi.ac.uk/pdbsum/5c6m PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DEOC_SHEHH DEOC_SHEHH]] Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Understanding enzyme stability and activity in extremophilic organisms is of great biotechnological interest, but many questions are still unsolved. Using 2-deoxy-D-ribose-5-phosphate aldolase (DERA) as model enzyme, we have evaluated structural and functional characteristics of different orthologs from psychrophilic, mesophilic and hyperthermophilic organisms. We present the first crystal structures of psychrophilic DERAs, revealing a dimeric organization resembling their mesophilic but not their thermophilic counterparts. Conversion into monomeric proteins showed that the native dimer interface contributes to stability only in the hyperthermophilic enzymes. Nevertheless, introduction of a disulfide bridge in the interface of a psychrophilic DERA did confer increased thermostability, suggesting a strategy for rational design of more durable enzyme variants. Constraint network analysis revealed particularly sparse interactions between the substrate pocket and its surrounding alpha-helices in psychrophilic DERAs, which indicates that a more flexible active center underlies their high turnover numbers.

-	~~The entry 5c6m is ON HOLD until Paper Publication~~	+	Trading off stability against activity in extremophilic aldolases.,Dick M, Weiergraber OH, Classen T, Bisterfeld C, Bramski J, Gohlke H, Pietruszka J Sci Rep. 2016 Jan 19;6:17908. doi: 10.1038/srep17908. PMID:26783049<ref>PMID:26783049</ref>

-	~~Authors: Weiergraeber~~, O.H.~~, Dick, M., Bramski, J., Pietruszka, J~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of deoxyribose-phosphate aldolase from Shewanella halifaxensis~~	+	<div class="pdbe-citations 5c6m" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Deoxyribose-phosphate aldolase]]
	[[Category: Bramski, J]]		[[Category: Bramski, J]]
-	[[Category: ~~Weiergraeber~~, ~~O.H~~]]	+	[[Category: Dick, M]]
	[[Category: Pietruszka, J]]		[[Category: Pietruszka, J]]
-	[[Category: ~~Dick~~, M]]	+	[[Category: Weiergraeber, O H]]
		+	[[Category: Dera]]
		+	[[Category: Lyase]]
		+	[[Category: Psychrophilic]]
		+	[[Category: Tim barrel]]

OCA: Protected "5c6m" [edit=sysop:move=sysop]

OCA — Wed, 01 Jul 2015 11:13:07 GMT

Protected "5c6m" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:13, 1 July 2015

OCA: New page: '''Unreleased structure''' The entry 5c6m is ON HOLD until Paper Publication Authors: Weiergraeber, O.H., Dick, M., Bramski, J., Pietruszka, J. Description: Crystal structure of deoxyr...

OCA — Wed, 01 Jul 2015 11:13:05 GMT

New page: '''Unreleased structure''' The entry 5c6m is ON HOLD until Paper Publication Authors: Weiergraeber, O.H., Dick, M., Bramski, J., Pietruszka, J. Description: Crystal structure of deoxyr...

New page

'''Unreleased structure'''

The entry 5c6m is ON HOLD until Paper Publication

Authors: Weiergraeber, O.H., Dick, M., Bramski, J., Pietruszka, J.

Description: Crystal structure of deoxyribose-phosphate aldolase from Shewanella halifaxensis
[[Category: Unreleased Structures]]
[[Category: Bramski, J]]
[[Category: Weiergraeber, O.H]]
[[Category: Pietruszka, J]]
[[Category: Dick, M]]