7pw1 - Revision history

OCA at 13:10, 1 February 2024

OCA — Thu, 01 Feb 2024 13:10:00 GMT

←Older revision		Revision as of 13:10, 1 February 2024
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	<StructureSection load='7pw1' size='340' side='right'caption='[[7pw1]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='7pw1' size='340' side='right'caption='[[7pw1]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7pw1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PW1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7pw1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PW1 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=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.5Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Haloalkane_dehalogenase Haloalkane dehalogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.5 3.8.1.5] </span></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=EDO:1,2-ETHANEDIOL'>EDO</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=7pw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pw1 OCA], [https://pdbe.org/7pw1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pw1 RCSB], [https://www.ebi.ac.uk/pdbsum/7pw1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pw1 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=7pw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pw1 OCA], [https://pdbe.org/7pw1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pw1 RCSB], [https://www.ebi.ac.uk/pdbsum/7pw1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pw1 ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 7pw1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7pw1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dehalogenase 3D structures\|Dehalogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Haloalkane dehalogenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Grinkevich, P~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Mazur, A~~]]	+	[[Category: Grinkevich P]]
-	[[Category: ~~Prudnikova, T~~]]	+	[[Category: Mazur A]]
-	[[Category: ~~Ancestral enzyme]]~~	+	[[Category: Prudnikova T]]
-	~~[[Category: Balbe]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 10:20, 13 April 2022

OCA — Wed, 13 Apr 2022 10:20:39 GMT

←Older revision		Revision as of 10:20, 13 April 2022
Line 1:		Line 1:

	==Crystal structure of ancestral haloalkane dehalogenase AncLinB-DmbA==		==Crystal structure of ancestral haloalkane dehalogenase AncLinB-DmbA==
-	<StructureSection load='7pw1' size='340' side='right'caption='[[7pw1]]' scene=''>	+	<StructureSection load='7pw1' size='340' side='right'caption='[[7pw1]], [[Resolution\|resolution]] 1.50Å' 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=7PW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PW1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7pw1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PW1 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=7pw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pw1 OCA], [https://pdbe.org/7pw1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pw1 RCSB], [https://www.ebi.ac.uk/pdbsum/7pw1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pw1 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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'>[https://en.wikipedia.org/wiki/Haloalkane_dehalogenase Haloalkane dehalogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.5 3.8.1.5] </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=7pw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pw1 OCA], [https://pdbe.org/7pw1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pw1 RCSB], [https://www.ebi.ac.uk/pdbsum/7pw1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pw1 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Haloalkane dehalogenases (EC 3.8.1.5) play an important role in hydrolytic degradation of halogenated compounds, resulting in a halide ion, a proton, and an alcohol. They are used in biocatalysis, bioremediation, and biosensing of environmental pollutants and also for molecular tagging in cell biology. The method of ancestral sequence reconstruction leads to prediction of sequences of ancestral enzymes allowing their experimental characterization. Based on the sequences of modern haloalkane dehalogenases from the subfamily II, the most common ancestor of thoroughly characterized enzymes LinB from Sphingobium japonicum UT26 and DmbA from Mycobacterium bovis 5033/66 was in silico predicted, recombinantly produced and structurally characterized. The ancestral enzyme AncLinB-DmbA was crystallized using the sitting-drop vapor-diffusion method, yielding rod-like crystals that diffracted X-rays to 1.5 A resolution. Structural comparison of AncLinB-DmbA with their closely related descendants LinB and DmbA revealed some differences in overall structure and tunnel architecture. Newly prepared AncLinB-DmbA has the highest active site cavity volume and the biggest entrance radius on the main tunnel in comparison to descendant enzymes. Ancestral sequence reconstruction is a powerful technique to study molecular evolution and design robust proteins for enzyme technologies.
		+
		+	Structural Analysis of the Ancestral Haloalkane Dehalogenase AncLinB-DmbA.,Mazur A, Grinkevich P, Chaloupkova R, Havlickova P, Kascakova B, Kuty M, Damborsky J, Kuta Smatanova I, Prudnikova T Int J Mol Sci. 2021 Nov 5;22(21). pii: ijms222111992. doi: 10.3390/ijms222111992. PMID:34769421<ref>PMID:34769421</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7pw1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Haloalkane dehalogenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Grinkevich P]]	+	[[Category: Grinkevich, P]]
-	[[Category: Mazur A]]	+	[[Category: Mazur, A]]
-	[[Category: Prudnikova T]]	+	[[Category: Prudnikova, T]]
		+	[[Category: Ancestral enzyme]]
		+	[[Category: Balbe]]
		+	[[Category: Hydrolase]]

OCA at 10:24, 6 April 2022

OCA — Wed, 06 Apr 2022 10:24:43 GMT

←Older revision		Revision as of 10:24, 6 April 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7pw1 ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of ancestral haloalkane dehalogenase AncLinB-DmbA==
-		+	<StructureSection load='7pw1' size='340' side='right'caption='[[7pw1]]' scene=''>
-	~~Authors~~: ~~Mazur~~, A., ~~Grinkevich~~, P., ~~Prudnikova~~, T.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PW1 FirstGlance]. <br>
-	~~Description: Crystal structure of ancestral haloalkane dehalogenase AncLinB-DmbA~~	+	</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=7pw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pw1 OCA], [https://pdbe.org/7pw1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pw1 RCSB], [https://www.ebi.ac.uk/pdbsum/7pw1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pw1 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Grinkevich, P]]	+	__TOC__
-	[[Category: ~~Prudnikova, T~~]]	+	</StructureSection>
-	[[Category: ~~Mazur, A~~]]	+	[[Category: Large Structures]]
		+	[[Category: Grinkevich P]]
		+	[[Category: Mazur A]]
		+	[[Category: Prudnikova T]]

OCA at 09:27, 30 March 2022

OCA — Wed, 30 Mar 2022 09:27:19 GMT

←Older revision		Revision as of 09:27, 30 March 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7pw1 is ON HOLD	+	The entry 7pw1 is ON HOLD until Paper Publication

	Authors: Mazur, A., Grinkevich, P., Prudnikova, T.		Authors: Mazur, A., Grinkevich, P., Prudnikova, T.

OCA at 04:56, 2 March 2022

OCA — Wed, 02 Mar 2022 04:56:24 GMT

←Older revision		Revision as of 04:56, 2 March 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7pw1 is ON HOLD ~~until sometime in the future~~	+	The entry 7pw1 is ON HOLD

	Authors: Mazur, A., Grinkevich, P., Prudnikova, T.		Authors: Mazur, A., Grinkevich, P., Prudnikova, T.

OCA: Protected "7pw1" [edit=sysop:move=sysop]

OCA — Wed, 13 Oct 2021 10:16:29 GMT

Protected "7pw1" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:16, 13 October 2021

OCA: New page: '''Unreleased structure''' The entry 7pw1 is ON HOLD until sometime in the future Authors: Mazur, A., Grinkevich, P., Prudnikova, T. Description: Crystal structure of ancestral haloalk...

OCA — Wed, 13 Oct 2021 10:16:28 GMT

New page: '''Unreleased structure''' The entry 7pw1 is ON HOLD until sometime in the future Authors: Mazur, A., Grinkevich, P., Prudnikova, T. Description: Crystal structure of ancestral haloalk...

New page

'''Unreleased structure'''

The entry 7pw1 is ON HOLD until sometime in the future

Authors: Mazur, A., Grinkevich, P., Prudnikova, T.

Description: Crystal structure of ancestral haloalkane dehalogenase AncLinB-DmbA
[[Category: Unreleased Structures]]
[[Category: Grinkevich, P]]
[[Category: Prudnikova, T]]
[[Category: Mazur, A]]