5wr4 - Revision history

OCA at 10:03, 6 September 2023

OCA — Wed, 06 Sep 2023 10:03:10 GMT

←Older revision		Revision as of 10:03, 6 September 2023
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	==Thermolysin, SFX unliganded form with oil-based carrier==		==Thermolysin, SFX unliganded form with oil-based carrier==
-	<StructureSection load='5wr4' size='340' side='right' caption='[[5wr4]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5wr4' size='340' side='right'caption='[[5wr4]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wr4]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_12980 Atcc 12980~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WR4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5WR4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wr4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WR4 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.1Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wr6\|5wr6]]~~, [[~~5wr5~~\|~~5wr5]], [[5wr3\|5wr3]], [[5wr2\|5wr2~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>nprS, nprM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1422 ATCC 12980])</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=5wr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wr4 OCA], [https://pdbe.org/5wr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wr4 RCSB], [https://www.ebi.ac.uk/pdbsum/5wr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wr4 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/Thermolysin Thermolysin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.27 3.4.24.27]~~ </~~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=5wr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wr4 OCA], [~~http~~://pdbe.org/5wr4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5wr4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5wr4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5wr4 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/THER_GEOSE THER_GEOSE]] Extracellular zinc metalloprotease.<ref>PMID:3149972</ref>	+	[https://www.uniprot.org/uniprot/THER_GEOSE THER_GEOSE] Extracellular zinc metalloprotease.<ref>PMID:3149972</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Thermolysin\|Thermolysin]]	+	*[[Thermolysin 3D structures\|Thermolysin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 12980~~]]	+	[[Category: Geobacillus stearothermophilus]]
-	[[Category: ~~Thermolysin~~]]	+	[[Category: Large Structures]]
-	[[Category: Kunishima, N]]	+	[[Category: Kunishima N]]
-	[[Category: Matsuura, Y]]	+	[[Category: Matsuura Y]]
-	[[Category: Naitow, H]]	+	[[Category: Naitow H]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Microcrystal]]~~	+
-	~~[[Category: Serial femtosecond crystallography]]~~	+
-	~~[[Category: Structure-based drug design]]~~	+
-	~~[[Category: X-ray free-electron laser~~]]	+

OCA at 20:50, 24 January 2018

OCA — Wed, 24 Jan 2018 20:50:31 GMT

←Older revision		Revision as of 20:50, 24 January 2018
Line 3:		Line 3:
	<StructureSection load='5wr4' size='340' side='right' caption='[[5wr4]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5wr4' size='340' side='right' caption='[[5wr4]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wr4]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WR4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WR4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wr4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WR4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WR4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wr6\|5wr6]], [[5wr5\|5wr5]], [[5wr3\|5wr3]], [[5wr2\|5wr2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wr6\|5wr6]], [[5wr5\|5wr5]], [[5wr3\|5wr3]], [[5wr2\|5wr2]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nprS, nprM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thermolysin Thermolysin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.27 3.4.24.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thermolysin Thermolysin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.27 3.4.24.27] </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=5wr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wr4 OCA], [http://pdbe.org/5wr4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wr4 RCSB], [http://www.ebi.ac.uk/pdbsum/5wr4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wr4 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=5wr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wr4 OCA], [http://pdbe.org/5wr4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wr4 RCSB], [http://www.ebi.ac.uk/pdbsum/5wr4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wr4 ProSAT]</span></td></tr>
Line 27:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 12980]]
	[[Category: Thermolysin]]		[[Category: Thermolysin]]
	[[Category: Kunishima, N]]		[[Category: Kunishima, N]]

OCA at 00:20, 16 November 2017

OCA — Thu, 16 Nov 2017 00:20:07 GMT

←Older revision		Revision as of 00:20, 16 November 2017
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5wr4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5wr4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thermolysin\|Thermolysin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:03, 17 August 2017

OCA — Thu, 17 Aug 2017 06:03:14 GMT

←Older revision		Revision as of 06:03, 17 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5wr4 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Thermolysin, SFX unliganded form with oil-based carrier==
		+	<StructureSection load='5wr4' size='340' side='right' caption='[[5wr4]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5wr4]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WR4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WR4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wr6\|5wr6]], [[5wr5\|5wr5]], [[5wr3\|5wr3]], [[5wr2\|5wr2]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thermolysin Thermolysin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.27 3.4.24.27] </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=5wr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wr4 OCA], [http://pdbe.org/5wr4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wr4 RCSB], [http://www.ebi.ac.uk/pdbsum/5wr4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wr4 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/THER_GEOSE THER_GEOSE]] Extracellular zinc metalloprotease.<ref>PMID:3149972</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Serial femtosecond crystallography (SFX) with an X-ray free-electron laser is used for the structural determination of proteins from a large number of microcrystals at room temperature. To examine the feasibility of pharmaceutical applications of SFX, a ligand-soaking experiment using thermolysin microcrystals has been performed using SFX. The results were compared with those from a conventional experiment with synchrotron radiation (SR) at 100 K. A protein-ligand complex structure was successfully obtained from an SFX experiment using microcrystals soaked with a small-molecule ligand; both oil-based and water-based crystal carriers gave essentially the same results. In a comparison of the SFX and SR structures, clear differences were observed in the unit-cell parameters, in the alternate conformation of side chains, in the degree of water coordination and in the ligand-binding mode.

-	~~Authors: Kunishima, N~~., Naitow, H., Matsuura, Y.	+	Protein-ligand complex structure from serial femtosecond crystallography using soaked thermolysin microcrystals and comparison with structures from synchrotron radiation.,Naitow H, Matsuura Y, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Tanaka R, Tanaka T, Sugahara M, Kobayashi J, Nango E, Iwata S, Kunishima N Acta Crystallogr D Struct Biol. 2017 Aug 1;73(Pt 8):702-709. doi:, 10.1107/S2059798317008919. Epub 2017 Jul 31. PMID:28777085<ref>PMID:28777085</ref>

-	~~Description: Thermolysin~~, ~~SFX unliganded form with oil-based carrier~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Naitow, H]]~~	+	<div class="pdbe-citations 5wr4" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Matsuura, Y~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Thermolysin]]
	[[Category: Kunishima, N]]		[[Category: Kunishima, N]]
		+	[[Category: Matsuura, Y]]
		+	[[Category: Naitow, H]]
		+	[[Category: Hydrolase]]
		+	[[Category: Microcrystal]]
		+	[[Category: Serial femtosecond crystallography]]
		+	[[Category: Structure-based drug design]]
		+	[[Category: X-ray free-electron laser]]

OCA at 19:47, 15 March 2017

OCA — Wed, 15 Mar 2017 19:47:52 GMT

←Older revision		Revision as of 19:47, 15 March 2017
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	Description: Thermolysin, SFX unliganded form with oil-based carrier		Description: Thermolysin, SFX unliganded form with oil-based carrier
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Naitow, H]]
	[[Category: Matsuura, Y]]		[[Category: Matsuura, Y]]
	[[Category: Kunishima, N]]		[[Category: Kunishima, N]]
-	[[Category: Naitow, H]]

OCA at 15:46, 4 January 2017

OCA — Wed, 04 Jan 2017 15:46:52 GMT

←Older revision		Revision as of 15:46, 4 January 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5wr4 is ON HOLD	+	The entry 5wr4 is ON HOLD until Paper Publication

	Authors: Kunishima, N., Naitow, H., Matsuura, Y.		Authors: Kunishima, N., Naitow, H., Matsuura, Y.

OCA: Protected "5wr4" [edit=sysop:move=sysop]

OCA — Fri, 09 Dec 2016 18:18:55 GMT

Protected "5wr4" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:18, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5wr4 is ON HOLD Authors: Kunishima, N., Naitow, H., Matsuura, Y. Description: Thermolysin, SFX unliganded form with oil-based carrier [[Category: U...

OCA — Fri, 09 Dec 2016 18:18:54 GMT

New page: '''Unreleased structure''' The entry 5wr4 is ON HOLD Authors: Kunishima, N., Naitow, H., Matsuura, Y. Description: Thermolysin, SFX unliganded form with oil-based carrier [[Category: U...

New page

'''Unreleased structure'''

The entry 5wr4 is ON HOLD

Authors: Kunishima, N., Naitow, H., Matsuura, Y.

Description: Thermolysin, SFX unliganded form with oil-based carrier
[[Category: Unreleased Structures]]
[[Category: Matsuura, Y]]
[[Category: Kunishima, N]]
[[Category: Naitow, H]]