5ldr - Revision history

OCA at 08:57, 11 October 2023

OCA — Wed, 11 Oct 2023 08:57:06 GMT

←Older revision		Revision as of 08:57, 11 October 2023
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	<StructureSection load='5ldr' size='340' side='right'caption='[[5ldr]], [[Resolution\|resolution]] 3.15Å' scene=''>		<StructureSection load='5ldr' size='340' side='right'caption='[[5ldr]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ldr]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Paracoccus_sp._32d Paracoccus sp. 32d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LDR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5LDR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ldr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_sp._32d Paracoccus sp. 32d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LDR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 3.15Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5euv\|5euv]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </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=5ldr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ldr OCA], [https://pdbe.org/5ldr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ldr RCSB], [https://www.ebi.ac.uk/pdbsum/5ldr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ldr 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=5ldr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ldr OCA], [~~http~~://pdbe.org/5ldr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ldr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ldr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ldr ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D1LZK0_9RHOB D1LZK0_9RHOB]
	<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: Beta-galactosidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Paracoccus sp. 32d]]		[[Category: Paracoccus sp. 32d]]
-	[[Category: Bujacz, A]]	+	[[Category: Bujacz A]]
-	[[Category: Bujacz, G]]	+	[[Category: Bujacz G]]
-	[[Category: Pietrzyk~~, A J~~]]	+	[[Category: Pietrzyk AJ]]
-	[[Category: Rutkiewicz-Krotewicz, M]]	+	[[Category: Rutkiewicz-Krotewicz M]]
-	[[Category: Sekula, B]]	+	[[Category: Sekula B]]
-	~~[[Category: Beta-d-galactosidase]]~~	+
-	~~[[Category: Cold-adapted]]~~	+
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Dimeric]]~~	+
-	~~[[Category: Galactose]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 12:24, 17 July 2019

OCA — Wed, 17 Jul 2019 12:24:52 GMT

←Older revision		Revision as of 12:24, 17 July 2019
Line 1:		Line 1:

	==Crystal structure of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d strain in complex with galactose==		==Crystal structure of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d strain in complex with galactose==
-	<StructureSection load='5ldr' size='340' side='right' caption='[[5ldr]], [[Resolution\|resolution]] 3.15Å' scene=''>	+	<StructureSection load='5ldr' size='340' side='right'caption='[[5ldr]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ldr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paracoccus_sp._32d Paracoccus sp. 32d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LDR FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ldr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paracoccus_sp._32d Paracoccus sp. 32d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LDR FirstGlance]. <br>
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5ldr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ldr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Galactosidase 3D structures\|Galactosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Beta-galactosidase]]		[[Category: Beta-galactosidase]]
		+	[[Category: Large Structures]]
	[[Category: Paracoccus sp. 32d]]		[[Category: Paracoccus sp. 32d]]
	[[Category: Bujacz, A]]		[[Category: Bujacz, A]]

OCA at 07:39, 6 December 2017

OCA — Wed, 06 Dec 2017 07:39:31 GMT

←Older revision		Revision as of 07:39, 6 December 2017
Line 3:		Line 3:
	<StructureSection load='5ldr' size='340' side='right' caption='[[5ldr]], [[Resolution\|resolution]] 3.15Å' scene=''>		<StructureSection load='5ldr' size='340' side='right' caption='[[5ldr]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ldr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LDR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ldr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paracoccus_sp._32d Paracoccus sp. 32d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LDR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5euv\|5euv]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5euv\|5euv]]</td></tr>
Line 9:		Line 9:
	<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=5ldr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ldr OCA], [http://pdbe.org/5ldr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ldr RCSB], [http://www.ebi.ac.uk/pdbsum/5ldr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ldr 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=5ldr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ldr OCA], [http://pdbe.org/5ldr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ldr RCSB], [http://www.ebi.ac.uk/pdbsum/5ldr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ldr ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of a novel dimeric beta-D-galactosidase from Paracoccus sp. 32d (ParbetaDG) was solved in space group P212121 at a resolution of 2.4 A by molecular replacement with multiple models using the BALBES software. This enzyme belongs to glycoside hydrolase family 2 (GH2), similar to the tetrameric and hexameric beta-D-galactosidases from Escherichia coli and Arthrobacter sp. C2-2, respectively. It is the second known structure of a cold-active GH2 beta-galactosidase, and the first in the form of a functional dimer, which is also present in the asymmetric unit. Cold-adapted beta-D-galactosidases have been the focus of extensive research owing to their utility in a variety of industrial technologies. One of their most appealing applications is in the hydrolysis of lactose, which not only results in the production of lactose-free dairy, but also eliminates the `sandy effect' and increases the sweetness of the product, thus enhancing its quality. The determined crystal structure represents the five-domain architecture of the enzyme, with its active site located in close vicinity to the dimer interface. To identify the amino-acid residues involved in the catalytic reaction and to obtain a better understanding of the mechanism of action of this atypical beta-D-galactosidase, the crystal structure in complex with galactose (ParbetaDG-Gal) was also determined. The catalytic site of the enzyme is created by amino-acid residues from the central domain 3 and from domain 4 of an adjacent monomer. The crystal structure of this dimeric beta-D-galactosidase reveals significant differences in comparison to other beta-galactosidases. The largest difference is in the fifth domain, named Bgal_windup domain 5 in ParbetaDG, which contributes to stabilization of the functional dimer. The location of this domain 5, which is unique in size and structure, may be one of the factors responsible for the creation of a functional dimer and cold-adaptation of this enzyme.
		+
		+	Structural studies of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d.,Rutkiewicz-Krotewicz M, Pietrzyk-Brzezinska AJ, Sekula B, Cieslinski H, Wierzbicka-Wos A, Kur J, Bujacz A Acta Crystallogr D Struct Biol. 2016 Sep;72(Pt 9):1049-61. doi:, 10.1107/S2059798316012535. Epub 2016 Aug 31. PMID:27599737<ref>PMID:27599737</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ldr" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Beta-galactosidase]]		[[Category: Beta-galactosidase]]
		+	[[Category: Paracoccus sp. 32d]]
	[[Category: Bujacz, A]]		[[Category: Bujacz, A]]
	[[Category: Bujacz, G]]		[[Category: Bujacz, G]]

OCA at 15:36, 14 September 2016

OCA — Wed, 14 Sep 2016 15:36:19 GMT

←Older revision		Revision as of 15:36, 14 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ldr ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d strain in complex with galactose==
-		+	<StructureSection load='5ldr' size='340' side='right' caption='[[5ldr]], [[Resolution\|resolution]] 3.15Å' scene=''>
-	~~Authors~~: ~~Rutkiewicz~~-~~Krotewicz, M~~., ~~Bujacz~~, A., ~~Pietrzyk~~, A.J., ~~Sekula~~, B., ~~Bujacz~~, G.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ldr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LDR FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of a cold-adapted dimeric beta-D~~-galactosidase ~~from Paracoccus sp. 32d strain in complex with galactose~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5euv\|5euv]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </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=5ldr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ldr OCA], [http://pdbe.org/5ldr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ldr RCSB], [http://www.ebi.ac.uk/pdbsum/5ldr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ldr ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-galactosidase]]
		+	[[Category: Bujacz, A]]
		+	[[Category: Bujacz, G]]
		+	[[Category: Pietrzyk, A J]]
	[[Category: Rutkiewicz-Krotewicz, M]]		[[Category: Rutkiewicz-Krotewicz, M]]
-	[[Category: Bujacz, G]]
-	[[Category: Pietrzyk, A.J]]
	[[Category: Sekula, B]]		[[Category: Sekula, B]]
-	[[Category: ~~Bujacz, A~~]]	+	[[Category: Beta-d-galactosidase]]
		+	[[Category: Cold-adapted]]
		+	[[Category: Complex]]
		+	[[Category: Dimeric]]
		+	[[Category: Galactose]]
		+	[[Category: Hydrolase]]

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

OCA — Wed, 13 Jul 2016 01:01:33 GMT

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

←Older revision

Revision as of 01:01, 13 July 2016

OCA: New page: '''Unreleased structure''' The entry 5ldr is ON HOLD until Paper Publication Authors: Rutkiewicz-Krotewicz, M., Bujacz, A., Pietrzyk, A.J., Sekula, B., Bujacz, G. Description: Crystal ...

OCA — Wed, 13 Jul 2016 01:01:31 GMT

New page: '''Unreleased structure''' The entry 5ldr is ON HOLD until Paper Publication Authors: Rutkiewicz-Krotewicz, M., Bujacz, A., Pietrzyk, A.J., Sekula, B., Bujacz, G. Description: Crystal ...

New page

'''Unreleased structure'''

The entry 5ldr is ON HOLD until Paper Publication

Authors: Rutkiewicz-Krotewicz, M., Bujacz, A., Pietrzyk, A.J., Sekula, B., Bujacz, G.

Description: Crystal structure of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d strain in complex with galactose
[[Category: Unreleased Structures]]
[[Category: Rutkiewicz-Krotewicz, M]]
[[Category: Bujacz, G]]
[[Category: Pietrzyk, A.J]]
[[Category: Sekula, B]]
[[Category: Bujacz, A]]