6d5p - Revision history

OCA at 14:32, 13 March 2024

2024-03-13T14:32:36Z

←Older revision		Revision as of 14:32, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6d5p' size='340' side='right'caption='[[6d5p]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='6d5p' size='340' side='right'caption='[[6d5p]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6d5p]] 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=6D5P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6D5P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6d5p]] 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=6D5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6D5P 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=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=VAL:VALINE'>VAL</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</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]] 3.0001087Å</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='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=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=VAL:VALINE'>VAL</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6d5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d5p OCA], [~~http~~://pdbe.org/6d5p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6d5p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6d5p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6d5p 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=6d5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d5p OCA], [https://pdbe.org/6d5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6d5p RCSB], [https://www.ebi.ac.uk/pdbsum/6d5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6d5p 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 of macromolecular crystals is commonly employed to limit radiation damage during X-ray diffraction data collection. However, cooling itself affects macromolecular conformation and often damages crystals via poorly understood processes. Here, the effects of cryosolution thermal contraction on macromolecular conformation and crystal order in crystals ranging from 32 to 67% solvent content are systematically investigated. It is found that the solution thermal contraction affects macromolecule configurations and volumes, unit-cell volumes, crystal packing and crystal order. The effects occur through not only thermal contraction, but also pressure caused by the mismatched contraction of cryosolvent and pores. Higher solvent-content crystals are more affected. In some cases the solvent contraction can be adjusted to reduce mosaicity and increase the strength of diffraction. Ice formation in some crystals is found to cause damage via a reduction in unit-cell volume, which is interpreted through solvent transport out of unit cells during cooling. The results point to more deductive approaches to cryoprotection optimization by adjusting the cryosolution composition to reduce thermal contraction-induced stresses in the crystal with cooling.	+
-		+
-	The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order.,Juers DH, Farley CA, Saxby CP, Cotter RA, Cahn JKB, Holton-Burke RC, Harrison K, Wu Z Acta Crystallogr D Struct Biol. 2018 Sep 1;74(Pt 9):922-938. doi:, 10.1107/S2059798318008793. Epub 2018 Sep 5. PMID:30198901<ref>PMID:30198901</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6d5p" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
-	*[[Thermolysin\|Thermolysin]]	+	*[[Thermolysin 3D structures\|Thermolysin 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Bacillus thermoproteolyticus]]		[[Category: Bacillus thermoproteolyticus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Thermolysin]]~~	+	[[Category: Juers DH]]
-	[[Category: Juers~~, D H]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Zinc protease~~]]	+

OCA at 10:56, 1 January 2020

2020-01-01T10:56:12Z

←Older revision		Revision as of 10:56, 1 January 2020
Line 1:		Line 1:

	==Hexagonal thermolysin cryocooled to 100 K with 20% xylose as cryoprotectant==		==Hexagonal thermolysin cryocooled to 100 K with 20% xylose as cryoprotectant==
-	<StructureSection load='6d5p' size='340' side='right' caption='[[6d5p]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='6d5p' size='340' side='right'caption='[[6d5p]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6d5p]] 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=6D5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D5P FirstGlance]. <br>		<table><tr><td colspan='2'>[[6d5p]] 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=6D5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D5P FirstGlance]. <br>
Line 27:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus thermoproteolyticus]]		[[Category: Bacillus thermoproteolyticus]]
		+	[[Category: Large Structures]]
	[[Category: Thermolysin]]		[[Category: Thermolysin]]
	[[Category: Juers, D H]]		[[Category: Juers, D H]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Zinc protease]]		[[Category: Zinc protease]]

OCA at 07:12, 31 October 2018

2018-10-31T07:12:37Z

←Older revision		Revision as of 07:12, 31 October 2018
Line 10:		Line 10:
	== 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 of macromolecular crystals is commonly employed to limit radiation damage during X-ray diffraction data collection. However, cooling itself affects macromolecular conformation and often damages crystals via poorly understood processes. Here, the effects of cryosolution thermal contraction on macromolecular conformation and crystal order in crystals ranging from 32 to 67% solvent content are systematically investigated. It is found that the solution thermal contraction affects macromolecule configurations and volumes, unit-cell volumes, crystal packing and crystal order. The effects occur through not only thermal contraction, but also pressure caused by the mismatched contraction of cryosolvent and pores. Higher solvent-content crystals are more affected. In some cases the solvent contraction can be adjusted to reduce mosaicity and increase the strength of diffraction. Ice formation in some crystals is found to cause damage via a reduction in unit-cell volume, which is interpreted through solvent transport out of unit cells during cooling. The results point to more deductive approaches to cryoprotection optimization by adjusting the cryosolution composition to reduce thermal contraction-induced stresses in the crystal with cooling.
		+
		+	The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order.,Juers DH, Farley CA, Saxby CP, Cotter RA, Cahn JKB, Holton-Burke RC, Harrison K, Wu Z Acta Crystallogr D Struct Biol. 2018 Sep 1;74(Pt 9):922-938. doi:, 10.1107/S2059798318008793. Epub 2018 Sep 5. PMID:30198901<ref>PMID:30198901</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6d5p" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thermolysin\|Thermolysin]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 19:48, 19 September 2018

2018-09-19T19:48:22Z

←Older revision		Revision as of 19:48, 19 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6d5p is ON HOLD~~	+	==Hexagonal thermolysin cryocooled to 100 K with 20% xylose as cryoprotectant==
-		+	<StructureSection load='6d5p' size='340' side='right' caption='[[6d5p]], [[Resolution\|resolution]] 3.00Å' scene=''>
-	~~Authors: Juers, D.H.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6d5p]] 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=6D5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D5P FirstGlance]. <br>
-	~~Description:~~ Hexagonal thermolysin cryocooled to 100 K with 20% xylose as cryoprotectant	+	</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=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=VAL:VALINE'>VAL</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</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>
-	[[Category: Juers, D.H]]	+	<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=6d5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d5p OCA], [http://pdbe.org/6d5p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d5p RCSB], [http://www.ebi.ac.uk/pdbsum/6d5p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d5p ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/THER_BACTH THER_BACTH]] Extracellular zinc metalloprotease.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bacillus thermoproteolyticus]]
		+	[[Category: Thermolysin]]
		+	[[Category: Juers, D H]]
		+	[[Category: Hydrolase]]
		+	[[Category: Zinc protease]]

OCA at 04:01, 16 May 2018

2018-05-16T04:01:00Z

←Older revision		Revision as of 04:01, 16 May 2018
Line 5:		Line 5:
	Authors: Juers, D.H.		Authors: Juers, D.H.

-	Description: ~~Tetragonal~~ thermolysin cryocooled to 100 K with 20% xylose as cryoprotectant	+	Description: Hexagonal thermolysin cryocooled to 100 K with 20% xylose as cryoprotectant
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Juers, D.H]]		[[Category: Juers, D.H]]

OCA: Protected "6d5p" [edit=sysop:move=sysop]

2018-04-25T04:14:44Z

Protected "6d5p" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:14, 25 April 2018

OCA: New page: '''Unreleased structure''' The entry 6d5p is ON HOLD Authors: Juers, D.H. Description: Tetragonal thermolysin cryocooled to 100 K with 20% xylose as cryoprotectant [[Category: Unreleas...

2018-04-25T04:14:42Z

New page: '''Unreleased structure''' The entry 6d5p is ON HOLD Authors: Juers, D.H. Description: Tetragonal thermolysin cryocooled to 100 K with 20% xylose as cryoprotectant [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 6d5p is ON HOLD

Authors: Juers, D.H.

Description: Tetragonal thermolysin cryocooled to 100 K with 20% xylose as cryoprotectant
[[Category: Unreleased Structures]]
[[Category: Juers, D.H]]