6i7z - Revision history

OCA at 11:48, 24 January 2024

OCA — Wed, 24 Jan 2024 11:48:56 GMT

←Older revision		Revision as of 11:48, 24 January 2024
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	<StructureSection load='6i7z' size='340' side='right'caption='[[6i7z]], [[Resolution\|resolution]] 1.78Å' scene=''>		<StructureSection load='6i7z' size='340' side='right'caption='[[6i7z]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6i7z]] is a 2 chain structure with sequence from [~~http~~://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=6I7Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6I7Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6i7z]] 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=6I7Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I7Z 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]] 1.78Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~SLIV_26340 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=457428 Streptomyces lividans TK24])~~</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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6i7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i7z OCA], [~~http~~://pdbe.org/6i7z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6i7z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6i7z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6i7z 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=6i7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i7z OCA], [https://pdbe.org/6i7z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i7z RCSB], [https://www.ebi.ac.uk/pdbsum/6i7z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i7z 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: Streptomyces lividans ~~tk24~~]]	+	[[Category: Streptomyces lividans TK24]]
-	[[Category: Appleby, M]]	+	[[Category: Appleby M]]
-	[[Category: Axford, D]]	+	[[Category: Axford D]]
-	[[Category: Ebrahim, A]]	+	[[Category: Ebrahim A]]
-	[[Category: Moreno-Chicano, T]]	+	[[Category: Moreno-Chicano T]]
-	[[Category: Owen~~, R L~~]]	+	[[Category: Owen RL]]
-	[[Category: Sherrell~~, D A~~]]	+	[[Category: Sherrell DA]]
-	[[Category: Strange~~, R W~~]]	+	[[Category: Strange RW]]
-	[[Category: Worrall~~, J A.R]]~~	+	[[Category: Worrall JAR]]
-	~~[[Category: Dose series]]~~	+
-	~~[[Category: Dye type peroxidase]]~~	+
-	~~[[Category: Heme]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Serial crystallography~~]]	+

OCA at 17:21, 14 August 2019

OCA — Wed, 14 Aug 2019 17:21:33 GMT

←Older revision		Revision as of 17:21, 14 August 2019
Line 3:		Line 3:
	<StructureSection load='6i7z' size='340' side='right'caption='[[6i7z]], [[Resolution\|resolution]] 1.78Å' scene=''>		<StructureSection load='6i7z' size='340' side='right'caption='[[6i7z]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6i7z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I7Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I7Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6i7z]] is a 2 chain structure with sequence from [http://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=6I7Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I7Z 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='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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SLIV_26340 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=457428 Streptomyces lividans TK24])</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=6i7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i7z OCA], [http://pdbe.org/6i7z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i7z RCSB], [http://www.ebi.ac.uk/pdbsum/6i7z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i7z 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=6i7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i7z OCA], [http://pdbe.org/6i7z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i7z RCSB], [http://www.ebi.ac.uk/pdbsum/6i7z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i7z ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Streptomyces lividans tk24]]
	[[Category: Appleby, M]]		[[Category: Appleby, M]]
	[[Category: Axford, D]]		[[Category: Axford, D]]

OCA at 06:16, 31 July 2019

OCA — Wed, 31 Jul 2019 06:16:29 GMT

←Older revision		Revision as of 06:16, 31 July 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6i7z is ~~ON HOLD until Paper~~ Publication	+	==Dye type peroxidase Aa from Streptomyces lividans: 32.8 kGy structure==
		+	<StructureSection load='6i7z' size='340' side='right'caption='[[6i7z]], [[Resolution\|resolution]] 1.78Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6i7z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I7Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I7Z 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=6i7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i7z OCA], [http://pdbe.org/6i7z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i7z RCSB], [http://www.ebi.ac.uk/pdbsum/6i7z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i7z 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: 32~~.~~8 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 6i7z" 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 05:03, 12 December 2018

OCA — Wed, 12 Dec 2018 05:03:48 GMT

←Older revision		Revision as of 05:03, 12 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6i7z is ON HOLD	+	The entry 6i7z 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.

OCA at 04:58, 5 December 2018

OCA — Wed, 05 Dec 2018 04:58:23 GMT

←Older revision		Revision as of 04:58, 5 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6i7z is ON HOLD ~~until Paper Publication~~	+	The entry 6i7z 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.		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: 32.8 kGy structure		Description: Dye type peroxidase Aa from Streptomyces lividans: 32.8 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 "6i7z" [edit=sysop:move=sysop]

OCA — Sun, 02 Dec 2018 18:43:33 GMT

Protected "6i7z" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:43, 2 December 2018

OCA: New page: '''Unreleased structure''' The entry 6i7z is ON HOLD until Paper Publication Authors: Ebrahim, A., Moreno-Chicano, T., Worrall, J.A.R., Strange, R.W., Axford, D., Sherrell, D.A., Appleb...

OCA — Sun, 02 Dec 2018 18:43:31 GMT

New page: '''Unreleased structure''' The entry 6i7z is ON HOLD until Paper Publication Authors: Ebrahim, A., Moreno-Chicano, T., Worrall, J.A.R., Strange, R.W., Axford, D., Sherrell, D.A., Appleb...

New page

'''Unreleased structure'''

The entry 6i7z 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.

Description: Dye type peroxidase Aa from Streptomyces lividans: 32.8 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]]