6n4w - Revision history

OCA at 14:46, 13 March 2024

2024-03-13T14:46:36Z

←Older revision		Revision as of 14:46, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6n4w' size='340' side='right'caption='[[6n4w]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='6n4w' size='340' side='right'caption='[[6n4w]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n4w]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~'bacillus_thermoproteolyticus' 'bacillus~~ thermoproteolyticus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N4W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6N4W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n4w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_thermoproteolyticus Bacillus thermoproteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N4W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N4W 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=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</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]] 1.4Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">npr ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1427 'Bacillus thermoproteolyticus'])</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=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=6n4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n4w OCA], [https://pdbe.org/6n4w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n4w RCSB], [https://www.ebi.ac.uk/pdbsum/6n4w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n4w 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=6n4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n4w OCA], [~~http~~://pdbe.org/6n4w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6n4w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6n4w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6n4w ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/THER_BACTH THER_BACTH]] Extracellular zinc metalloprotease.	+	[https://www.uniprot.org/uniprot/THER_BACTH THER_BACTH] Extracellular zinc metalloprotease.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Cryocooling for macromolecular crystallography is usually performed via plunging the crystal into a liquid cryogen or placing the crystal in a cold gas stream. These two approaches are compared here for the case of nitro-gen cooling. The results show that gas stream cooling, which typically cools the crystal more slowly, yields lower mosaicity and, in some cases, a stronger anomalous signal relative to rapid plunge cooling. During plunging, moving the crystal slowly through the cold gas layer above the liquid surface can produce mosaicity similar to gas stream cooling. Annealing plunge cooled crystals by warming and recooling in the gas stream allows the mosaicity and anomalous signal to recover. For tetragonal thermolysin, the observed effects are less pronounced when the cryosolvent has smaller thermal contraction, under which conditions the protein structures from plunge cooled and gas stream cooled crystals are very similar. Finally, this work also demonstrates that the resolution dependence of the reflecting range is correlated with the cooling method, suggesting it may be a useful tool for discerning whether crystals are cooled too rapidly. The results support previous studies suggesting that slower cooling methods are less deleterious to crystal order, as long as ice formation is prevented and dehydration is limited.	+

-	A comparison of gas stream cooling and plunge cooling of macromolecular crystals.,Harrison K, Wu Z, Juers DH J Appl Crystallogr. 2019 Aug 23;52(Pt 5):1222-1232. doi:, 10.1107/S1600576719010318. eCollection 2019 Oct 1. PMID:31636524<ref>PMID:31636524</ref>	+	==See Also==
-		+	*[[Thermolysin 3D structures\|Thermolysin 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6n4w" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Bacillus thermoproteolyticus]]		[[Category: Bacillus thermoproteolyticus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Thermolysin]]~~	+	[[Category: Harrison K]]
-	[[Category: Harrison, K]]	+	[[Category: Juers DH]]
-	[[Category: Juers~~, D H~~]]	+	[[Category: Wu B]]
-	[[Category: Wu, B]]	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Zinc protease~~]]	+

OCA at 08:26, 6 November 2019

2019-11-06T08:26:27Z

←Older revision		Revision as of 08:26, 6 November 2019
Line 3:		Line 3:
	<StructureSection load='6n4w' size='340' side='right'caption='[[6n4w]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='6n4w' size='340' side='right'caption='[[6n4w]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n4w]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N4W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N4W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n4w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/'bacillus_thermoproteolyticus' 'bacillus thermoproteolyticus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N4W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N4W 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=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</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=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</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">npr ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1427 'Bacillus thermoproteolyticus'])</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=6n4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n4w OCA], [http://pdbe.org/6n4w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n4w RCSB], [http://www.ebi.ac.uk/pdbsum/6n4w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n4w 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=6n4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n4w OCA], [http://pdbe.org/6n4w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n4w RCSB], [http://www.ebi.ac.uk/pdbsum/6n4w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n4w ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/THER_BACTH THER_BACTH]] Extracellular zinc metalloprotease.		[[http://www.uniprot.org/uniprot/THER_BACTH THER_BACTH]] Extracellular zinc metalloprotease.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cryocooling for macromolecular crystallography is usually performed via plunging the crystal into a liquid cryogen or placing the crystal in a cold gas stream. These two approaches are compared here for the case of nitro-gen cooling. The results show that gas stream cooling, which typically cools the crystal more slowly, yields lower mosaicity and, in some cases, a stronger anomalous signal relative to rapid plunge cooling. During plunging, moving the crystal slowly through the cold gas layer above the liquid surface can produce mosaicity similar to gas stream cooling. Annealing plunge cooled crystals by warming and recooling in the gas stream allows the mosaicity and anomalous signal to recover. For tetragonal thermolysin, the observed effects are less pronounced when the cryosolvent has smaller thermal contraction, under which conditions the protein structures from plunge cooled and gas stream cooled crystals are very similar. Finally, this work also demonstrates that the resolution dependence of the reflecting range is correlated with the cooling method, suggesting it may be a useful tool for discerning whether crystals are cooled too rapidly. The results support previous studies suggesting that slower cooling methods are less deleterious to crystal order, as long as ice formation is prevented and dehydration is limited.
		+
		+	A comparison of gas stream cooling and plunge cooling of macromolecular crystals.,Harrison K, Wu Z, Juers DH J Appl Crystallogr. 2019 Aug 23;52(Pt 5):1222-1232. doi:, 10.1107/S1600576719010318. eCollection 2019 Oct 1. PMID:31636524<ref>PMID:31636524</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6n4w" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus thermoproteolyticus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Thermolysin]]		[[Category: Thermolysin]]

OCA at 10:27, 2 October 2019

2019-10-02T10:27:47Z

←Older revision		Revision as of 10:27, 2 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6n4w is ON HOLD until Paper Publication~~	+	==Tetragonal thermolysin (with 50% xylose) cryocooled in a nitrogen gas stream to 100 K==
-		+	<StructureSection load='6n4w' size='340' side='right'caption='[[6n4w]], [[Resolution\|resolution]] 1.40Å' scene=''>
-	~~Authors: Juers, D.H., Harrison, K., Wu, B.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6n4w]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N4W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N4W FirstGlance]. <br>
-	~~Description:~~ Tetragonal thermolysin (with 50% xylose) cryocooled in a nitrogen gas stream to 100 K	+	</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=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6n4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n4w OCA], [http://pdbe.org/6n4w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n4w RCSB], [http://www.ebi.ac.uk/pdbsum/6n4w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n4w ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/THER_BACTH THER_BACTH]] Extracellular zinc metalloprotease.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Thermolysin]]
		+	[[Category: Harrison, K]]
		+	[[Category: Juers, D H]]
	[[Category: Wu, B]]		[[Category: Wu, B]]
-	[[Category: ~~Harrison, K~~]]	+	[[Category: Hydrolase]]
-	[[Category: ~~Juers, D.H~~]]	+	[[Category: Zinc protease]]

OCA at 06:44, 26 December 2018

2018-12-26T06:44:51Z

←Older revision		Revision as of 06:44, 26 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6n4w is ON HOLD	+	The entry 6n4w is ON HOLD until Paper Publication

	Authors: Juers, D.H., Harrison, K., Wu, B.		Authors: Juers, D.H., Harrison, K., Wu, B.

OCA: Protected "6n4w" [edit=sysop:move=sysop]

2018-12-02T19:16:49Z

Protected "6n4w" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:16, 2 December 2018

OCA: New page: '''Unreleased structure''' The entry 6n4w is ON HOLD Authors: Juers, D.H., Harrison, K., Wu, B. Description: Tetragonal thermolysin (with 50% xylose) cryocooled in a nitrogen gas strea...

2018-12-02T19:16:47Z

New page: '''Unreleased structure''' The entry 6n4w is ON HOLD Authors: Juers, D.H., Harrison, K., Wu, B. Description: Tetragonal thermolysin (with 50% xylose) cryocooled in a nitrogen gas strea...

New page

'''Unreleased structure'''

The entry 6n4w is ON HOLD

Authors: Juers, D.H., Harrison, K., Wu, B.

Description: Tetragonal thermolysin (with 50% xylose) cryocooled in a nitrogen gas stream to 100 K
[[Category: Unreleased Structures]]
[[Category: Wu, B]]
[[Category: Harrison, K]]
[[Category: Juers, D.H]]