6qrw - Revision history

OCA at 12:07, 24 January 2024

OCA — Wed, 24 Jan 2024 12:07:21 GMT

←Older revision		Revision as of 12:07, 24 January 2024
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	<StructureSection load='6qrw' size='340' side='right'caption='[[6qrw]], [[Resolution\|resolution]] 1.17Å' scene=''>		<StructureSection load='6qrw' size='340' side='right'caption='[[6qrw]], [[Resolution\|resolution]] 1.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qrw]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QRW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6QRW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qrw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QRW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QRW 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=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 1.17Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </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=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6qrw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qrw OCA], [~~http~~://pdbe.org/6qrw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6qrw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6qrw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6qrw 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=6qrw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qrw OCA], [https://pdbe.org/6qrw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qrw RCSB], [https://www.ebi.ac.uk/pdbsum/6qrw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qrw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/XYLA_STRRU XYLA_STRRU]] Involved in D-xylose catabolism.	+	[https://www.uniprot.org/uniprot/XYLA_STRRU XYLA_STRRU] Involved in D-xylose catabolism.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6qrw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6qrw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[D-xylose isomerase 3D structures\|D-xylose isomerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Xylose isomerase~~]]	+	[[Category: Streptomyces rubiginosus]]
-	[[Category: Bury~~, C S~~]]	+	[[Category: Bury CS]]
-	[[Category: Garman~~, E F~~]]	+	[[Category: Garman EF]]
-	[[Category: Snell~~, E H~~]]	+	[[Category: Snell EH]]
-	[[Category: Taberman, H]]	+	[[Category: Taberman H]]
-	[[Category: Woerd~~, M J.van der]]~~	+	[[Category: Van der Woerd MJ]]
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Metal binding protein~~]]	+

OCA at 10:50, 17 July 2019

OCA — Wed, 17 Jul 2019 10:50:52 GMT

←Older revision		Revision as of 10:50, 17 July 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6qrw is ~~ON HOLD until Paper~~ Publication	+	==X-ray radiation dose series on xylose isomerase - 3.25 MGy==
		+	<StructureSection load='6qrw' size='340' side='right'caption='[[6qrw]], [[Resolution\|resolution]] 1.17Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6qrw]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QRW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QRW 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=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </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=6qrw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qrw OCA], [http://pdbe.org/6qrw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qrw RCSB], [http://www.ebi.ac.uk/pdbsum/6qrw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qrw ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/XYLA_STRRU XYLA_STRRU]] Involved in D-xylose catabolism.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Xylose isomerase (XI) is an industrially important metalloprotein studied for decades. Its reaction mechanism has been postulated to involve movement of the catalytic metal cofactor to several different conformations. Here, a dose-dependent approach was used to investigate the radiation damage effects on XI and their potential influence on the reaction mechanism interpreted from the X-ray derived structures. Radiation damage is still one of the major challenges for X-ray diffraction experiments and causes both global and site-specific damage. In this study, consecutive high-resolution data sets from a single XI crystal from the same wedge were collected at 100 K and the progression of radiation damage was tracked over increasing dose (0.13-3.88 MGy). The catalytic metal and its surrounding amino acid environment experience a build-up of free radicals, and the results show radiation-damage-induced structural perturbations ranging from an absolute metal positional shift to specific residue motions in the active site. The apparent metal movement is an artefact of global damage and the resulting unit-cell expansion, but residue motion appears to be driven by the dose. Understanding and identifying radiation-induced damage is an important factor in accurately interpreting the biological conclusions being drawn.

-	~~Authors~~:	+	Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both.,Taberman H, Bury CS, van der Woerd MJ, Snell EH, Garman EF J Synchrotron Radiat. 2019 Jul 1;26(Pt 4):931-944. doi:, 10.1107/S1600577519005599. Epub 2019 Jun 24. PMID:31274415<ref>PMID:31274415</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6qrw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Xylose isomerase]]
		+	[[Category: Bury, C S]]
		+	[[Category: Garman, E F]]
		+	[[Category: Snell, E H]]
		+	[[Category: Taberman, H]]
		+	[[Category: Woerd, M J.van der]]
		+	[[Category: Isomerase]]
		+	[[Category: Metal binding protein]]

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

OCA — Wed, 27 Feb 2019 14:00:03 GMT

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

←Older revision

Revision as of 14:00, 27 February 2019

OCA: New page: '''Unreleased structure''' The entry 6qrw is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Feb 2019 14:00:01 GMT

New page: '''Unreleased structure''' The entry 6qrw is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6qrw is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]