6i8k - Revision history

OCA at 11:49, 24 January 2024

OCA — Wed, 24 Jan 2024 11:49:20 GMT

←Older revision		Revision as of 11:49, 24 January 2024
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	<StructureSection load='6i8k' size='340' side='right'caption='[[6i8k]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='6i8k' size='340' side='right'caption='[[6i8k]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6i8k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I8K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6I8K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6i8k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_lividans_TK24 Streptomyces lividans TK24]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I8K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I8K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.98Å</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=6i8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i8k OCA], [~~http~~://pdbe.org/6i8k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6i8k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6i8k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6i8k ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=6i8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i8k OCA], [https://pdbe.org/6i8k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i8k RCSB], [https://www.ebi.ac.uk/pdbsum/6i8k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i8k ProSAT]</span></td></tr>
	</table>		</table>
-	== Function ==
-	[[http://www.uniprot.org/uniprot/A0A076MF68_STRLI A0A076MF68_STRLI]] Involved in the recovery of exogenous heme iron. Extracts iron from heme while preserving the tetrapyrrol ring intact.[RuleBase:RU365017]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Appleby, M]]	+	[[Category: Streptomyces lividans TK24]]
-	[[Category: Axford, D]]	+	[[Category: Appleby M]]
-	[[Category: Ebrahim, A]]	+	[[Category: Axford D]]
-	[[Category: Moreno-Chicano, T]]	+	[[Category: Ebrahim A]]
-	[[Category: Owen~~, R L~~]]	+	[[Category: Moreno-Chicano T]]
-	[[Category: Sherrell~~, D A~~]]	+	[[Category: Owen RL]]
-	[[Category: Strange~~, R W~~]]	+	[[Category: Sherrell DA]]
-	[[Category: Worrall~~, J A.R]]~~	+	[[Category: Strange RW]]
-	~~[[Category: Dose series]]~~	+	[[Category: Worrall JAR]]
-	~~[[Category: Dye type peroxidase]]~~	+
-	~~[[Category: Heme]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Serial crystallography~~]]	+

OCA at 06:16, 31 July 2019

OCA — Wed, 31 Jul 2019 06:16:58 GMT

←Older revision		Revision as of 06:16, 31 July 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6i8k is ~~ON HOLD until Paper~~ Publication	+	==Dye type peroxidase Aa from Streptomyces lividans: 164 kGy structure==
		+	<StructureSection load='6i8k' size='340' side='right'caption='[[6i8k]], [[Resolution\|resolution]] 1.98Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6i8k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I8K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I8K FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=6i8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i8k OCA], [http://pdbe.org/6i8k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i8k RCSB], [http://www.ebi.ac.uk/pdbsum/6i8k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i8k ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A076MF68_STRLI A0A076MF68_STRLI]] Involved in the recovery of exogenous heme iron. Extracts iron from heme while preserving the tetrapyrrol ring intact.[RuleBase:RU365017]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	An approach is demonstrated to obtain, in a sample- and time-efficient manner, multiple dose-resolved crystal structures from room-temperature protein microcrystals using identical fixed-target supports at both synchrotrons and X-ray free-electron lasers (XFELs). This approach allows direct comparison of dose-resolved serial synchrotron and damage-free XFEL serial femtosecond crystallography structures of radiation-sensitive proteins. Specifically, serial synchrotron structures of a heme peroxidase enzyme reveal that X-ray induced changes occur at far lower doses than those at which diffraction quality is compromised (the Garman limit), consistent with previous studies on the reduction of heme proteins by low X-ray doses. In these structures, a functionally relevant bond length is shown to vary rapidly as a function of absorbed dose, with all room-temperature synchrotron structures exhibiting linear deformation of the active site compared with the XFEL structure. It is demonstrated that extrapolation of dose-dependent synchrotron structures to zero dose can closely approximate the damage-free XFEL structure. This approach is widely applicable to any protein where the crystal structure is altered by the synchrotron X-ray beam and provides a solution to the urgent requirement to determine intact structures of such proteins in a high-throughput and accessible manner.

-	~~Authors: Ebrahim~~, A., Moreno-Chicano, T., ~~Worrall~~, ~~J.A.R.~~, Strange, ~~R.W.~~, Axford, D., ~~Sherrell~~, D.A.~~, Appleby, M~~., ~~Owen, R.L~~.	+	Dose-resolved serial synchrotron and XFEL structures of radiation-sensitive metalloproteins.,Ebrahim A, Moreno-Chicano T, Appleby MV, Chaplin AK, Beale JH, Sherrell DA, Duyvesteyn HME, Owada S, Tono K, Sugimoto H, Strange RW, Worrall JAR, Axford D, Owen RL, Hough MA IUCrJ. 2019 May 3;6(Pt 4):543-551. doi: 10.1107/S2052252519003956. eCollection, 2019 Jul 1. PMID:31316799<ref>PMID:31316799</ref>

-	~~Description: Dye type peroxidase Aa from Streptomyces lividans: 164 kGy structure~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Ebrahim, A]]~~	+	<div class="pdbe-citations 6i8k" style="background-color:#fffaf0;"></div>
-	~~[[Category: Owen, R.L]]~~	+	== References ==
-	~~[[Category: Moreno-Chicano, T]]~~	+	<references/>
-	~~[[Category: Worrall, J.A.R]]~~	+	__TOC__
-	[[Category: ~~Strange, R.W~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Appleby, M]]		[[Category: Appleby, M]]
-	[[Category: Sherrell, D.A]]
	[[Category: Axford, D]]		[[Category: Axford, D]]
		+	[[Category: Ebrahim, A]]
		+	[[Category: Moreno-Chicano, T]]
		+	[[Category: Owen, R L]]
		+	[[Category: Sherrell, D A]]
		+	[[Category: Strange, R W]]
		+	[[Category: Worrall, J A.R]]
		+	[[Category: Dose series]]
		+	[[Category: Dye type peroxidase]]
		+	[[Category: Heme]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Serial crystallography]]

OCA at 05:04, 12 December 2018

OCA — Wed, 12 Dec 2018 05:04:03 GMT

←Older revision		Revision as of 05:04, 12 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6i8k is ON HOLD	+	The entry 6i8k is ON HOLD until Paper Publication

	Authors: Ebrahim, A., Moreno-Chicano, T., Worrall, J.A.R., Strange, R.W., Axford, D., Sherrell, D.A., Appleby, M., Owen, R.L.		Authors: Ebrahim, A., Moreno-Chicano, T., Worrall, J.A.R., Strange, R.W., Axford, D., Sherrell, D.A., Appleby, M., Owen, R.L.
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	Description: Dye type peroxidase Aa from Streptomyces lividans: 164 kGy structure		Description: Dye type peroxidase Aa from Streptomyces lividans: 164 kGy structure
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Worrall, J.A.R]]
-	[[Category: Sherrell, D.A]]
	[[Category: Ebrahim, A]]		[[Category: Ebrahim, A]]
	[[Category: Owen, R.L]]		[[Category: Owen, R.L]]
	[[Category: Moreno-Chicano, T]]		[[Category: Moreno-Chicano, T]]
		+	[[Category: Worrall, J.A.R]]
	[[Category: Strange, R.W]]		[[Category: Strange, R.W]]
	[[Category: Appleby, M]]		[[Category: Appleby, M]]
		+	[[Category: Sherrell, D.A]]
	[[Category: Axford, D]]		[[Category: Axford, D]]

OCA: Protected "6i8k" [edit=sysop:move=sysop]

OCA — Sun, 02 Dec 2018 18:45:10 GMT

Protected "6i8k" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:45, 2 December 2018

OCA: New page: '''Unreleased structure''' The entry 6i8k is ON HOLD Authors: Ebrahim, A., Moreno-Chicano, T., Worrall, J.A.R., Strange, R.W., Axford, D., Sherrell, D.A., Appleby, M., Owen, R.L. Descr...

OCA — Sun, 02 Dec 2018 18:45:09 GMT

New page: '''Unreleased structure''' The entry 6i8k is ON HOLD Authors: Ebrahim, A., Moreno-Chicano, T., Worrall, J.A.R., Strange, R.W., Axford, D., Sherrell, D.A., Appleby, M., Owen, R.L. Descr...

New page

'''Unreleased structure'''

The entry 6i8k is ON HOLD

Authors: Ebrahim, A., Moreno-Chicano, T., Worrall, J.A.R., Strange, R.W., Axford, D., Sherrell, D.A., Appleby, M., Owen, R.L.

Description: Dye type peroxidase Aa from Streptomyces lividans: 164 kGy structure
[[Category: Unreleased Structures]]
[[Category: Worrall, J.A.R]]
[[Category: Sherrell, D.A]]
[[Category: Ebrahim, A]]
[[Category: Owen, R.L]]
[[Category: Moreno-Chicano, T]]
[[Category: Strange, R.W]]
[[Category: Appleby, M]]
[[Category: Axford, D]]