5mcf - Revision history

OCA at 18:38, 1 November 2023

OCA — Wed, 01 Nov 2023 18:38:20 GMT

←Older revision		Revision as of 18:38, 1 November 2023
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	<StructureSection load='5mcf' size='340' side='right'caption='[[5mcf]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5mcf' size='340' side='right'caption='[[5mcf]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mcf]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Dappu Dappu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MCF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5MCF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mcf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Daphnia_pulex Daphnia pulex]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MCF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MCF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'>GOL</scene~~>, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~PCA~~:~~PYROGLUTAMIC+ACID~~'>~~PCA~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">CEL7A~~, ~~DAPPUDRAFT_347598 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6669 DAPPU])~~<~~/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=5mcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mcf OCA], [https://pdbe.org/5mcf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mcf RCSB], [https://www.ebi.ac.uk/pdbsum/5mcf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mcf 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/Cellulose_1,4-beta-cellobiosidase_(non-reducing_end) Cellulose 1,4-beta-cellobiosidase (non-reducing end)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.91 3.2.1.91] </~~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=5mcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mcf OCA], [~~http~~://pdbe.org/5mcf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5mcf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5mcf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5mcf ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/E9G5J5_DAPPU E9G5J5_DAPPU]
	<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: ~~Dappu~~]]	+	[[Category: Daphnia pulex]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bury~~, C S~~]]	+	[[Category: Bury CS]]
-	[[Category: Ebrahim, A]]	+	[[Category: Ebrahim A]]
-	[[Category: Garman~~, E F~~]]	+	[[Category: Garman EF]]
-	[[Category: McGeehan~~, J E]]~~	+	[[Category: McGeehan JE]]
-	~~[[Category: Cellobiohydrolase]]~~	+
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Radiation damage~~]]	+

OCA at 07:46, 11 March 2020

OCA — Wed, 11 Mar 2020 07:46:10 GMT

←Older revision		Revision as of 07:46, 11 March 2020
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	==Radiation damage to GH7 Family Cellobiohydrolase from Daphnia pulex: Dose (DWD) 7.59 MGy==		==Radiation damage to GH7 Family Cellobiohydrolase from Daphnia pulex: Dose (DWD) 7.59 MGy==
-	<StructureSection load='5mcf' size='340' side='right' caption='[[5mcf]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5mcf' size='340' side='right'caption='[[5mcf]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mcf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MCF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MCF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mcf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Dappu Dappu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MCF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MCF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CEL7A, DAPPUDRAFT_347598 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6669 DAPPU])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cellulose_1,4-beta-cellobiosidase_(non-reducing_end) Cellulose 1,4-beta-cellobiosidase (non-reducing end)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.91 3.2.1.91] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cellulose_1,4-beta-cellobiosidase_(non-reducing_end) Cellulose 1,4-beta-cellobiosidase (non-reducing end)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.91 3.2.1.91] </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=5mcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mcf OCA], [http://pdbe.org/5mcf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mcf RCSB], [http://www.ebi.ac.uk/pdbsum/5mcf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mcf 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=5mcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mcf OCA], [http://pdbe.org/5mcf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mcf RCSB], [http://www.ebi.ac.uk/pdbsum/5mcf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mcf ProSAT]</span></td></tr>
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	==See Also==		==See Also==
-	*[[Cellobiohydrolase\|Cellobiohydrolase]]	+	*[[Cellobiohydrolase 3D structures\|Cellobiohydrolase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Dappu]]
		+	[[Category: Large Structures]]
	[[Category: Bury, C S]]		[[Category: Bury, C S]]
	[[Category: Ebrahim, A]]		[[Category: Ebrahim, A]]

OCA at 10:48, 13 September 2017

OCA — Wed, 13 Sep 2017 10:48:42 GMT

←Older revision		Revision as of 10:48, 13 September 2017
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	</div>		</div>
	<div class="pdbe-citations 5mcf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5mcf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cellobiohydrolase\|Cellobiohydrolase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:34, 18 January 2017

OCA — Wed, 18 Jan 2017 16:34:57 GMT

←Older revision		Revision as of 16:34, 18 January 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5mcf is ~~ON HOLD~~	+	==Radiation damage to GH7 Family Cellobiohydrolase from Daphnia pulex: Dose (DWD) 7.59 MGy==
		+	<StructureSection load='5mcf' size='340' side='right' caption='[[5mcf]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5mcf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MCF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MCF FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cellulose_1,4-beta-cellobiosidase_(non-reducing_end) Cellulose 1,4-beta-cellobiosidase (non-reducing end)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.91 3.2.1.91] </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=5mcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mcf OCA], [http://pdbe.org/5mcf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mcf RCSB], [http://www.ebi.ac.uk/pdbsum/5mcf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mcf ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	During macromolecular X-ray crystallography experiments, protein crystals held at 100 K have been widely reported to exhibit reproducible bond scission events at doses on the order of several MGy. With the objective to mitigate the impact of radiation damage events on valid structure determination, it is essential to correctly understand the radiation chemistry mechanisms at play. OH-cleavage from tyrosine residues is regularly cited as amongst the most available damage pathways in protein crystals at 100 K, despite a lack of widespread reports of this phenomenon in protein crystal radiation damage studies. Furthermore, no clear mechanism for phenolic C-O bond cleavage in tyrosine has been reported, with the tyrosyl radical known to be relatively robust and long-lived in both aqueous solutions and the solid state. Here, the initial findings of Tyr -OH group damage in a myrosinase protein crystal have been reviewed. Consistent with that study, at increasing doses, clear electron density loss was detectable local to Tyr -OH groups. A systematic investigation performed on a range of protein crystal damage series deposited in the Protein Data Bank has established that Tyr -OH electron density loss is not generally a dominant damage pathway in protein crystals at 100 K. Full Tyr aromatic ring displacement is here proposed to account for instances of observable Tyr -OH electron density loss, with the original myrosinase data shown to be consistent with such a damage model. Systematic analysis of the effects of other environmental factors, including solvent accessibility and proximity to disulfide bonds or hydrogen bond interactions, is also presented. Residues in known active sites showed enhanced sensitivity to radiation-induced disordering, as has previously been reported.

-	~~Authors~~: ~~Bury, C.S~~., ~~McGeehan~~, J.E.~~, Ebrahim, A~~., ~~Garman, E.F~~.	+	OH cleavage from tyrosine: debunking a myth.,Bury CS, Carmichael I, Garman EF J Synchrotron Radiat. 2017 Jan 1;24(Pt 1):7-18. doi: 10.1107/S1600577516016775., Epub 2017 Jan 1. PMID:28009542<ref>PMID:28009542</ref>

-	~~Description: Radiation damage to GH7 Family Cellobiohydrolase from Daphnia pulex: Dose (DWD) 7~~.~~59 MGy~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Garman~~, ~~E.F~~]]	+	<div class="pdbe-citations 5mcf" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bury, C S]]
	[[Category: Ebrahim, A]]		[[Category: Ebrahim, A]]
-	[[Category: ~~Bury~~, ~~C.S~~]]	+	[[Category: Garman, E F]]
-	[[Category: ~~Mcgeehan~~, J.E]]	+	[[Category: McGeehan, J E]]
		+	[[Category: Cellobiohydrolase]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Radiation damage]]

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

OCA — Fri, 09 Dec 2016 16:38:41 GMT

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

←Older revision

Revision as of 16:38, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5mcf is ON HOLD Authors: Bury, C.S., McGeehan, J.E., Ebrahim, A., Garman, E.F. Description: Radiation damage to GH7 Family Cellobiohydrolase from D...

OCA — Fri, 09 Dec 2016 16:38:40 GMT

New page: '''Unreleased structure''' The entry 5mcf is ON HOLD Authors: Bury, C.S., McGeehan, J.E., Ebrahim, A., Garman, E.F. Description: Radiation damage to GH7 Family Cellobiohydrolase from D...

New page

'''Unreleased structure'''

The entry 5mcf is ON HOLD

Authors: Bury, C.S., McGeehan, J.E., Ebrahim, A., Garman, E.F.

Description: Radiation damage to GH7 Family Cellobiohydrolase from Daphnia pulex: Dose (DWD) 7.59 MGy
[[Category: Unreleased Structures]]
[[Category: Garman, E.F]]
[[Category: Ebrahim, A]]
[[Category: Bury, C.S]]
[[Category: Mcgeehan, J.E]]