6web - Revision history

OCA at 14:22, 18 October 2023

OCA — Wed, 18 Oct 2023 14:22:58 GMT

←Older revision		Revision as of 14:22, 18 October 2023
Line 1:		Line 1:

	==Multi-Hit SFX using MHz XFEL sources==		==Multi-Hit SFX using MHz XFEL sources==
-	<StructureSection load='6web' size='340' side='right'caption='[[6web]]' scene=''>	+	<StructureSection load='6web' size='340' side='right'caption='[[6web]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WEB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6web]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WEB FirstGlance]. <br>
-	</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=6web FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6web OCA], [https://pdbe.org/6web PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6web RCSB], [https://www.ebi.ac.uk/pdbsum/6web PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6web ProSAT]</span></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]] 2.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=6web FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6web OCA], [https://pdbe.org/6web PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6web RCSB], [https://www.ebi.ac.uk/pdbsum/6web PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6web ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work has shown that it is possible to use consecutive X-ray pulses to collect diffraction patterns from individual crystals. Here, we exploit the MHz pulse structure of the European XFEL to obtain two complete datasets from the same lysozyme crystal, first hit and the second hit, before it exits the beam. The two datasets, separated by <1 micros, yield up to 2.1 A resolution structures. Comparisons between the two structures reveal no indications of radiation damage or significant changes within the active site, consistent with the calculated dose estimates. This demonstrates MHz SFX can be used as a tool for tracking sub-microsecond structural changes in individual single crystals, a technique we refer to as multi-hit SFX.
		+
		+	Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers.,Holmes S, Kirkwood HJ, Bean R, Giewekemeyer K, Martin AV, Hadian-Jazi M, Wiedorn MO, Oberthur D, Marman H, Adriano L, Al-Qudami N, Bajt S, Barak I, Bari S, Bielecki J, Brockhauser S, Coleman MA, Cruz-Mazo F, Danilevski C, Dorner K, Ganan-Calvo AM, Graceffa R, Fanghor H, Heymann M, Frank M, Kaukher A, Kim Y, Kobe B, Knoska J, Laurus T, Letrun R, Maia L, Messerschmidt M, Metz M, Michelat T, Mills G, Molodtsov S, Monteiro DCF, Morgan AJ, Munnich A, Pena Murillo GE, Previtali G, Round A, Sato T, Schubert R, Schulz J, Shelby M, Seuring C, Sellberg JA, Sikorski M, Silenzi A, Stern S, Sztuk-Dambietz J, Szuba J, Trebbin M, Vagovic P, Ve T, Weinhausen B, Wrona K, Xavier PL, Xu C, Yefanov O, Nugent KA, Chapman HN, Mancuso AP, Barty A, Abbey B, Darmanin C Nat Commun. 2022 Aug 11;13(1):4708. doi: 10.1038/s41467-022-32434-6. PMID:35953469<ref>PMID:35953469</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6web" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]		*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Gallus gallus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Abbey B]]		[[Category: Abbey B]]
	[[Category: Darmanin C]]		[[Category: Darmanin C]]
	[[Category: Holmes S]]		[[Category: Holmes S]]

OCA at 11:00, 31 August 2022

OCA — Wed, 31 Aug 2022 11:00:43 GMT

←Older revision		Revision as of 11:00, 31 August 2022
Line 1:		Line 1:

	==Multi-Hit SFX using MHz XFEL sources==		==Multi-Hit SFX using MHz XFEL sources==
-	<StructureSection load='6web' size='340' side='right'caption='[[6web]]~~, [[Resolution\|resolution]] 2.10Å~~' scene=''>	+	<StructureSection load='6web' size='340' side='right'caption='[[6web]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[6web]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WEB FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WEB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>	+	</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=6web FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6web OCA], [https://pdbe.org/6web PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6web RCSB], [https://www.ebi.ac.uk/pdbsum/6web PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6web ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=6web FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6web OCA], [https://pdbe.org/6web PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6web RCSB], [https://www.ebi.ac.uk/pdbsum/6web PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6web ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work has shown that it is possible to use consecutive X-ray pulses to collect diffraction patterns from individual crystals. Here, we exploit the MHz pulse structure of the European XFEL to obtain two complete datasets from the same lysozyme crystal, first hit and the second hit, before it exits the beam. The two datasets, separated by <1 micros, yield up to 2.1 A resolution structures. Comparisons between the two structures reveal no indications of radiation damage or significant changes within the active site, consistent with the calculated dose estimates. This demonstrates MHz SFX can be used as a tool for tracking sub-microsecond structural changes in individual single crystals, a technique we refer to as multi-hit SFX.
-
-	Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers.,Holmes S, Kirkwood HJ, Bean R, Giewekemeyer K, Martin AV, Hadian-Jazi M, Wiedorn MO, Oberthur D, Marman H, Adriano L, Al-Qudami N, Bajt S, Barak I, Bari S, Bielecki J, Brockhauser S, Coleman MA, Cruz-Mazo F, Danilevski C, Dorner K, Ganan-Calvo AM, Graceffa R, Fanghor H, Heymann M, Frank M, Kaukher A, Kim Y, Kobe B, Knoska J, Laurus T, Letrun R, Maia L, Messerschmidt M, Metz M, Michelat T, Mills G, Molodtsov S, Monteiro DCF, Morgan AJ, Munnich A, Pena Murillo GE, Previtali G, Round A, Sato T, Schubert R, Schulz J, Shelby M, Seuring C, Sellberg JA, Sikorski M, Silenzi A, Stern S, Sztuk-Dambietz J, Szuba J, Trebbin M, Vagovic P, Ve T, Weinhausen B, Wrona K, Xavier PL, Xu C, Yefanov O, Nugent KA, Chapman HN, Mancuso AP, Barty A, Abbey B, Darmanin C Nat Commun. 2022 Aug 11;13(1):4708. doi: 10.1038/s41467-022-32434-6. PMID:35953469<ref>PMID:35953469</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6web" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]		*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Gallus gallus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lysozyme]]~~	+	[[Category: Abbey B]]
-	[[Category: Abbey, B]]	+	[[Category: Darmanin C]]
-	[[Category: Darmanin, C]]	+	[[Category: Holmes S]]
-	[[Category: Holmes, S]]	+
-	~~[[Category: Enzyme]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 05:09, 25 August 2022

OCA — Thu, 25 Aug 2022 05:09:27 GMT

←Older revision		Revision as of 05:09, 25 August 2022
Line 1:		Line 1:

	==Multi-Hit SFX using MHz XFEL sources==		==Multi-Hit SFX using MHz XFEL sources==
-	<StructureSection load='6web' size='340' side='right'caption='[[6web]]' scene=''>	+	<StructureSection load='6web' size='340' side='right'caption='[[6web]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WEB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6web]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WEB FirstGlance]. <br>
-	</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=6web FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6web OCA], [https://pdbe.org/6web PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6web RCSB], [https://www.ebi.ac.uk/pdbsum/6web PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6web ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=6web FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6web OCA], [https://pdbe.org/6web PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6web RCSB], [https://www.ebi.ac.uk/pdbsum/6web PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6web ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work has shown that it is possible to use consecutive X-ray pulses to collect diffraction patterns from individual crystals. Here, we exploit the MHz pulse structure of the European XFEL to obtain two complete datasets from the same lysozyme crystal, first hit and the second hit, before it exits the beam. The two datasets, separated by <1 micros, yield up to 2.1 A resolution structures. Comparisons between the two structures reveal no indications of radiation damage or significant changes within the active site, consistent with the calculated dose estimates. This demonstrates MHz SFX can be used as a tool for tracking sub-microsecond structural changes in individual single crystals, a technique we refer to as multi-hit SFX.
		+
		+	Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers.,Holmes S, Kirkwood HJ, Bean R, Giewekemeyer K, Martin AV, Hadian-Jazi M, Wiedorn MO, Oberthur D, Marman H, Adriano L, Al-Qudami N, Bajt S, Barak I, Bari S, Bielecki J, Brockhauser S, Coleman MA, Cruz-Mazo F, Danilevski C, Dorner K, Ganan-Calvo AM, Graceffa R, Fanghor H, Heymann M, Frank M, Kaukher A, Kim Y, Kobe B, Knoska J, Laurus T, Letrun R, Maia L, Messerschmidt M, Metz M, Michelat T, Mills G, Molodtsov S, Monteiro DCF, Morgan AJ, Munnich A, Pena Murillo GE, Previtali G, Round A, Sato T, Schubert R, Schulz J, Shelby M, Seuring C, Sellberg JA, Sikorski M, Silenzi A, Stern S, Sztuk-Dambietz J, Szuba J, Trebbin M, Vagovic P, Ve T, Weinhausen B, Wrona K, Xavier PL, Xu C, Yefanov O, Nugent KA, Chapman HN, Mancuso AP, Barty A, Abbey B, Darmanin C Nat Commun. 2022 Aug 11;13(1):4708. doi: 10.1038/s41467-022-32434-6. PMID:35953469<ref>PMID:35953469</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6web" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Gallus gallus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Abbey B]]	+	[[Category: Lysozyme]]
-	[[Category: Darmanin C]]	+	[[Category: Abbey, B]]
-	[[Category: Holmes S]]	+	[[Category: Darmanin, C]]
		+	[[Category: Holmes, S]]
		+	[[Category: Enzyme]]
		+	[[Category: Hydrolase]]

OCA at 11:39, 13 October 2021

OCA — Wed, 13 Oct 2021 11:39:35 GMT

←Older revision		Revision as of 11:39, 13 October 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6web is ~~ON HOLD until Paper Publication~~	+	==Multi-Hit SFX using MHz XFEL sources==
-		+	<StructureSection load='6web' size='340' side='right'caption='[[6web]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WEB FirstGlance]. <br>
-	~~Description~~:	+	</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=6web FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6web OCA], [https://pdbe.org/6web PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6web RCSB], [https://www.ebi.ac.uk/pdbsum/6web PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6web ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Abbey B]]
		+	[[Category: Darmanin C]]
		+	[[Category: Holmes S]]

OCA at 04:01, 13 May 2020

OCA — Wed, 13 May 2020 04:01:01 GMT

←Older revision		Revision as of 04:01, 13 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 08 Apr 2020 05:39:56 GMT

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

←Older revision

Revision as of 05:39, 8 April 2020

OCA: New page: '''Unreleased structure''' The entry 6web is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 08 Apr 2020 05:39:55 GMT

New page: '''Unreleased structure''' The entry 6web is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6web is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]