6i6g - Revision history

OCA at 11:47, 24 January 2024

2024-01-24T11:47:50Z

←Older revision		Revision as of 11:47, 24 January 2024
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	<StructureSection load='6i6g' size='340' side='right'caption='[[6i6g]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='6i6g' size='340' side='right'caption='[[6i6g]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6i6g]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I6G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6I6G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6i6g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I6G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I6G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H4N:5-bromanyl-1~{H}-indole'>H4N</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.85Å</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=6i6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i6g OCA], [~~http~~://pdbe.org/6i6g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6i6g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6i6g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6i6g ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=H4N:5-bromanyl-1~{H}-indole'>H4N</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6i6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i6g OCA], [https://pdbe.org/6i6g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i6g RCSB], [https://www.ebi.ac.uk/pdbsum/6i6g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i6g ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9NAV7_9ANNE Q9NAV7_9ANNE]
	<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 6i6g" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6i6g" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dehaloperoxidase 3D structures\|Dehaloperoxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 28:
	[[Category: Amphitrite ornata]]		[[Category: Amphitrite ornata]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Axford, D]]	+	[[Category: Axford D]]
-	[[Category: Duyvesteyn, H]]	+	[[Category: Duyvesteyn H]]
-	[[Category: Ebrahim~~, A E~~]]	+	[[Category: Ebrahim AE]]
-	[[Category: Moreno-Chicano, T]]	+	[[Category: Moreno-Chicano T]]
-	[[Category: Owada, S]]	+	[[Category: Owada S]]
-	[[Category: Sherrell~~, D A~~]]	+	[[Category: Sherrell DA]]
-	[[Category: Strange~~, R W~~]]	+	[[Category: Strange RW]]
-	[[Category: Sugimoto, H]]	+	[[Category: Sugimoto H]]
-	[[Category: Tono, K]]	+	[[Category: Tono K]]
-	[[Category: Worrall~~, J A.R]]~~	+	[[Category: Worrall JAR]]
-	~~[[Category: 5-bromoindole]]~~	+
-	~~[[Category: Globin]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Peroxidase~~]]	+

OCA at 16:33, 22 January 2020

2020-01-22T16:33:13Z

←Older revision		Revision as of 16:33, 22 January 2020
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	<StructureSection load='6i6g' size='340' side='right'caption='[[6i6g]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='6i6g' size='340' side='right'caption='[[6i6g]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6i6g]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I6G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I6G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6i6g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I6G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I6G FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H4N:5-bromanyl-1~{H}-indole'>H4N</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=H4N:5-bromanyl-1~{H}-indole'>H4N</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6i6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i6g OCA], [http://pdbe.org/6i6g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i6g RCSB], [http://www.ebi.ac.uk/pdbsum/6i6g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i6g 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=6i6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i6g OCA], [http://pdbe.org/6i6g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i6g RCSB], [http://www.ebi.ac.uk/pdbsum/6i6g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i6g ProSAT]</span></td></tr>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Amphitrite ornata]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Axford, D]]		[[Category: Axford, D]]

OCA at 15:20, 20 November 2019

2019-11-20T15:20:30Z

←Older revision		Revision as of 15:20, 20 November 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6i6g is ~~ON HOLD until Paper~~ Publication	+	==Dehaloperoxidase B from Amphitrite ornata - complex with 5-bromoindole==
		+	<StructureSection load='6i6g' size='340' side='right'caption='[[6i6g]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6i6g]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I6G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I6G FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H4N:5-bromanyl-1~{H}-indole'>H4N</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6i6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i6g OCA], [http://pdbe.org/6i6g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i6g RCSB], [http://www.ebi.ac.uk/pdbsum/6i6g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i6g ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	High-throughput X-ray crystal structures of protein-ligand complexes are critical to pharmaceutical drug development. However, cryocooling of crystals and X-ray radiation damage may distort the observed ligand binding. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) can produce radiation-damage-free room-temperature structures. Ligand-binding studies using SFX have received only modest attention, partly owing to limited beamtime availability and the large quantity of sample that is required per structure determination. Here, a high-throughput approach to determine room-temperature damage-free structures with excellent sample and time efficiency is demonstrated, allowing complexes to be characterized rapidly and without prohibitive sample requirements. This yields high-quality difference density maps allowing unambiguous ligand placement. Crucially, it is demonstrated that ligands similar in size or smaller than those used in fragment-based drug design may be clearly identified in data sets obtained from <1000 diffraction images. This efficiency in both sample and XFEL beamtime opens the door to true high-throughput screening of protein-ligand complexes using SFX.

-	~~Authors:~~ Moreno-Chicano, T., Ebrahim, A~~.E.~~, ~~Worrall~~, ~~J.A.R.~~, ~~Strange~~, ~~R.W.~~, ~~Axford~~, D., Sherrell, ~~D.A.~~, Sugimoto, H., Tono, K., ~~Owada~~, S., ~~Duyvesteyn, H~~.	+	High-throughput structures of protein-ligand complexes at room temperature using serial femtosecond crystallography.,Moreno-Chicano T, Ebrahim A, Axford D, Appleby MV, Beale JH, Chaplin AK, Duyvesteyn HME, Ghiladi RA, Owada S, Sherrell DA, Strange RW, Sugimoto H, Tono K, Worrall JAR, Owen RL, Hough MA IUCrJ. 2019 Oct 10;6(Pt 6):1074-1085. doi: 10.1107/S2052252519011655. eCollection, 2019 Nov 1. PMID:31709063<ref>PMID:31709063</ref>

-	~~Description: Dehaloperoxidase B from Amphitrite ornata -complex with 5-bromoindole~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category: Tono~~, ~~K]]~~	+	<div class="pdbe-citations 6i6g" style="background-color:#fffaf0;"></div>
-	~~[[Category: Sugimoto, H]]~~	+	== References ==
-	~~[[Category~~: ~~Ebrahim, A.E]]~~	+	<references/>
-	~~[[Category: Owada, S]]~~	+	__TOC__
-	~~[[Category: Moreno-Chicano, T]]~~	+	</StructureSection>
-	~~[[Category: Worrall, J.A.R]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Duyvesteyn, H]]~~	+
-	[[Category: ~~Strange, R.W]]~~	+
-	~~[[Category: Sherrell, D.A~~]]	+
	[[Category: Axford, D]]		[[Category: Axford, D]]
		+	[[Category: Duyvesteyn, H]]
		+	[[Category: Ebrahim, A E]]
		+	[[Category: Moreno-Chicano, T]]
		+	[[Category: Owada, S]]
		+	[[Category: Sherrell, D A]]
		+	[[Category: Strange, R W]]
		+	[[Category: Sugimoto, H]]
		+	[[Category: Tono, K]]
		+	[[Category: Worrall, J A.R]]
		+	[[Category: 5-bromoindole]]
		+	[[Category: Globin]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Peroxidase]]

OCA at 04:57, 5 December 2018

2018-12-05T04:57:42Z

←Older revision		Revision as of 04:57, 5 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6i6g is ON HOLD	+	The entry 6i6g is ON HOLD until Paper Publication

	Authors: Moreno-Chicano, T., Ebrahim, A.E., Worrall, J.A.R., Strange, R.W., Axford, D., Sherrell, D.A., Sugimoto, H., Tono, K., Owada, S., Duyvesteyn, H.		Authors: Moreno-Chicano, T., Ebrahim, A.E., Worrall, J.A.R., Strange, R.W., Axford, D., Sherrell, D.A., Sugimoto, H., Tono, K., Owada, S., Duyvesteyn, H.
Line 7:		Line 7:
	Description: Dehaloperoxidase B from Amphitrite ornata -complex with 5-bromoindole		Description: Dehaloperoxidase B from Amphitrite ornata -complex with 5-bromoindole
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Sugimoto, H]]
-	[[Category: Worrall, J.A.R]]
-	[[Category: Duyvesteyn, H]]
-	[[Category: Sherrell, D.A]]
	[[Category: Tono, K]]		[[Category: Tono, K]]
		+	[[Category: Sugimoto, H]]
	[[Category: Ebrahim, A.E]]		[[Category: Ebrahim, A.E]]
	[[Category: Owada, S]]		[[Category: Owada, S]]
	[[Category: Moreno-Chicano, T]]		[[Category: Moreno-Chicano, T]]
		+	[[Category: Worrall, J.A.R]]
		+	[[Category: Duyvesteyn, H]]
	[[Category: Strange, R.W]]		[[Category: Strange, R.W]]
		+	[[Category: Sherrell, D.A]]
	[[Category: Axford, D]]		[[Category: Axford, D]]

OCA: Protected "6i6g" [edit=sysop:move=sysop]

2018-12-02T18:38:37Z

Protected "6i6g" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:38, 2 December 2018

OCA: New page: '''Unreleased structure''' The entry 6i6g is ON HOLD Authors: Moreno-Chicano, T., Ebrahim, A.E., Worrall, J.A.R., Strange, R.W., Axford, D., Sherrell, D.A., Sugimoto, H., Tono, K., Owad...

2018-12-02T18:38:35Z

New page: '''Unreleased structure''' The entry 6i6g is ON HOLD Authors: Moreno-Chicano, T., Ebrahim, A.E., Worrall, J.A.R., Strange, R.W., Axford, D., Sherrell, D.A., Sugimoto, H., Tono, K., Owad...

New page

'''Unreleased structure'''

The entry 6i6g is ON HOLD

Authors: Moreno-Chicano, T., Ebrahim, A.E., Worrall, J.A.R., Strange, R.W., Axford, D., Sherrell, D.A., Sugimoto, H., Tono, K., Owada, S., Duyvesteyn, H.

Description: Dehaloperoxidase B from Amphitrite ornata -complex with 5-bromoindole
[[Category: Unreleased Structures]]
[[Category: Sugimoto, H]]
[[Category: Worrall, J.A.R]]
[[Category: Duyvesteyn, H]]
[[Category: Sherrell, D.A]]
[[Category: Tono, K]]
[[Category: Ebrahim, A.E]]
[[Category: Owada, S]]
[[Category: Moreno-Chicano, T]]
[[Category: Strange, R.W]]
[[Category: Axford, D]]