5tw0 - Revision history

OCA at 15:43, 6 March 2024

2024-03-06T15:43:36Z

←Older revision		Revision as of 15:43, 6 March 2024
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	==Structure of Pfp1 protease from Thermococcus thioreducens: small cell H3 crystal form==		==Structure of Pfp1 protease from Thermococcus thioreducens: small cell H3 crystal form==
-	<StructureSection load='5tw0' size='340' side='right' caption='[[5tw0]], [[Resolution\|resolution]] 1.96Å' scene=''>	+	<StructureSection load='5tw0' size='340' side='right'caption='[[5tw0]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tw0]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_baa-394 Atcc baa-394~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TW0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TW0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tw0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_thioreducens Thermococcus thioreducens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TW0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TW0 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</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]] 1.96Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5txw\|5txw]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">AMR53_10535 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=277988 ATCC BAA-394])~~</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=5tw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tw0 OCA], [https://pdbe.org/5tw0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tw0 RCSB], [https://www.ebi.ac.uk/pdbsum/5tw0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tw0 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=5tw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tw0 OCA], [~~http~~://pdbe.org/5tw0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tw0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tw0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tw0 ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0A0Q2XKL6_9EURY A0A0Q2XKL6_9EURY]
-	~~The Pfp1 protease, a cysteine protease of unknown specificity from the hyperthermophilic archaeon Thermococcus thioreducens, was crystallized in two distinctive crystal forms~~: from concentrated citrate in one case and PEG in the other. X-ray data were collected from both crystal forms at room temperature to about 1.9 A resolution using a laboratory source and detector, and the structures were solved by molecular replacement using the Pfp1 protease from Pyrococcus horikoshii as the search model. In the T. thioreducens protease structures, Cys18 residues on adjacent molecules in the asymmetric units form intermolecular disulfide bonds, thereby yielding hexamers composed of three cross-linked, quasi-dyad-related dimers with crystallographically exact threefold axes and exhibiting almost exact 32 symmetry. The corresponding residue in P. horikoshii Pfp1 is Tyr18. An individual active site containing Cys100 and His101 also includes a Glu74 residue contributed by a quasi-twofold-related, non-cross-linked subunit. Two catalytic triads are therefore closely juxtaposed about the quasi-twofold axis at the interface of these subunits, and are relatively sequestered within the hexamer cavity. The cysteine in the active site is observed to be oxidized in both of the crystal forms that were studied.	+
-		+
-	The structure of the Pfp1 protease from the hyperthermophilic archaeon Thermococcus thioreducens in two crystal forms.,Larson SB, McPherson A Acta Crystallogr D Struct Biol. 2017 Sep 1;73(Pt 9):749-756. doi:, 10.1107/~~S2059798317010622. Epub 2017 Aug 15. PMID:28876238<ref>PMID:28876238<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5tw0" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc baa-394~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Larson, S B~~]]	+	[[Category: Thermococcus thioreducens]]
-	[[Category: ~~McPherson, A~~]]	+	[[Category: Larson SB]]
-	[[Category: ~~Hexamer]]~~	+	[[Category: McPherson A]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Noncrystallographic symmetry]]~~	+
-	~~[[Category: Protease]]~~	+
-	~~[[Category: Thermophile~~]]	+

OCA at 06:31, 18 April 2018

2018-04-18T06:31:51Z

←Older revision		Revision as of 06:31, 18 April 2018
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	<StructureSection load='5tw0' size='340' side='right' caption='[[5tw0]], [[Resolution\|resolution]] 1.96Å' scene=''>		<StructureSection load='5tw0' size='340' side='right' caption='[[5tw0]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tw0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TW0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TW0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tw0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_baa-394 Atcc baa-394]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TW0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TW0 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5txw\|5txw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5txw\|5txw]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AMR53_10535 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=277988 ATCC BAA-394])</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=5tw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tw0 OCA], [http://pdbe.org/5tw0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tw0 RCSB], [http://www.ebi.ac.uk/pdbsum/5tw0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tw0 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=5tw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tw0 OCA], [http://pdbe.org/5tw0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tw0 RCSB], [http://www.ebi.ac.uk/pdbsum/5tw0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tw0 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Pfp1 protease, a cysteine protease of unknown specificity from the hyperthermophilic archaeon Thermococcus thioreducens, was crystallized in two distinctive crystal forms: from concentrated citrate in one case and PEG in the other. X-ray data were collected from both crystal forms at room temperature to about 1.9 A resolution using a laboratory source and detector, and the structures were solved by molecular replacement using the Pfp1 protease from Pyrococcus horikoshii as the search model. In the T. thioreducens protease structures, Cys18 residues on adjacent molecules in the asymmetric units form intermolecular disulfide bonds, thereby yielding hexamers composed of three cross-linked, quasi-dyad-related dimers with crystallographically exact threefold axes and exhibiting almost exact 32 symmetry. The corresponding residue in P. horikoshii Pfp1 is Tyr18. An individual active site containing Cys100 and His101 also includes a Glu74 residue contributed by a quasi-twofold-related, non-cross-linked subunit. Two catalytic triads are therefore closely juxtaposed about the quasi-twofold axis at the interface of these subunits, and are relatively sequestered within the hexamer cavity. The cysteine in the active site is observed to be oxidized in both of the crystal forms that were studied.
		+
		+	The structure of the Pfp1 protease from the hyperthermophilic archaeon Thermococcus thioreducens in two crystal forms.,Larson SB, McPherson A Acta Crystallogr D Struct Biol. 2017 Sep 1;73(Pt 9):749-756. doi:, 10.1107/S2059798317010622. Epub 2017 Aug 15. PMID:28876238<ref>PMID:28876238</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5tw0" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc baa-394]]
	[[Category: Larson, S B]]		[[Category: Larson, S B]]
	[[Category: McPherson, A]]		[[Category: McPherson, A]]

OCA at 05:29, 6 October 2017

2017-10-06T05:29:48Z

←Older revision		Revision as of 05:29, 6 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5tw0 is ~~ON HOLD until Paper Publication~~	+	==Structure of Pfp1 protease from Thermococcus thioreducens: small cell H3 crystal form==
-		+	<StructureSection load='5tw0' size='340' side='right' caption='[[5tw0]], [[Resolution\|resolution]] 1.96Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5tw0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TW0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TW0 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5txw\|5txw]]</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=5tw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tw0 OCA], [http://pdbe.org/5tw0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tw0 RCSB], [http://www.ebi.ac.uk/pdbsum/5tw0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tw0 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Larson, S B]]
		+	[[Category: McPherson, A]]
		+	[[Category: Hexamer]]
		+	[[Category: Hydrolase]]
		+	[[Category: Noncrystallographic symmetry]]
		+	[[Category: Protease]]
		+	[[Category: Thermophile]]

OCA: Protected "5tw0" [edit=sysop:move=sysop]

2016-12-09T17:57:42Z

Protected "5tw0" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:57, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5tw0 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2016-12-09T17:57:41Z

New page: '''Unreleased structure''' The entry 5tw0 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5tw0 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]