5oe9 - Revision history

OCA at 16:46, 13 December 2023

OCA — Wed, 13 Dec 2023 16:46:35 GMT

←Older revision		Revision as of 16:46, 13 December 2023
Line 3:		Line 3:
	<StructureSection load='5oe9' size='340' side='right'caption='[[5oe9]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='5oe9' size='340' side='right'caption='[[5oe9]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5oe9]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Deep-~~sea_thermophilic_bacteriophage_d6e~~ Deep-sea thermophilic ~~bacteriophage d6e~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OE9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5OE9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5oe9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Deep-sea_thermophilic_phage_D6E Deep-sea thermophilic phage D6E]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OE9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OE9 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.4Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5oe8\|5oe8]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5oe9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oe9 OCA], [~~http~~://pdbe.org/5oe9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5oe9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5oe9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5oe9 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=5oe9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oe9 OCA], [https://pdbe.org/5oe9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5oe9 RCSB], [https://www.ebi.ac.uk/pdbsum/5oe9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5oe9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/E5DV50_9CAUD E5DV50_9CAUD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 21:

	==See Also==		==See Also==
-	*[[Terminase\|Terminase]]	+	*[[Terminase 3D Structures\|Terminase 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Deep-sea thermophilic ~~bacteriophage d6e~~]]	+	[[Category: Deep-sea thermophilic phage D6E]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Antson~~, A A~~]]	+	[[Category: Antson AA]]
-	[[Category: Greive~~, S J~~]]	+	[[Category: Greive SJ]]
-	[[Category: Jenkins~~, H T~~]]	+	[[Category: Jenkins HT]]
-	[[Category: Xu~~, R G]]~~	+	[[Category: Xu RG]]
-	~~[[Category: Large terminase]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 12:22, 26 August 2020

OCA — Wed, 26 Aug 2020 12:22:13 GMT

←Older revision		Revision as of 12:22, 26 August 2020
Line 1:		Line 1:

	==Structure of large terminase from the thermophilic bacteriophage D6E in complex with sulfate (Crystal form 2)==		==Structure of large terminase from the thermophilic bacteriophage D6E in complex with sulfate (Crystal form 2)==
-	<StructureSection load='5oe9' size='340' side='right' caption='[[5oe9]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='5oe9' size='340' side='right'caption='[[5oe9]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5oe9]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Deep-sea_thermophilic_bacteriophage_d6e Deep-sea thermophilic bacteriophage d6e]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OE9 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OE9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5oe9]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Deep-sea_thermophilic_bacteriophage_d6e Deep-sea thermophilic bacteriophage d6e]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OE9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5OE9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5oe8\|5oe8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5oe8\|5oe8]]</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=5oe9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oe9 OCA], [http://pdbe.org/5oe9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oe9 RCSB], [http://www.ebi.ac.uk/pdbsum/5oe9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oe9 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5oe9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oe9 OCA], [http://pdbe.org/5oe9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oe9 RCSB], [http://www.ebi.ac.uk/pdbsum/5oe9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oe9 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5oe9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5oe9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Terminase\|Terminase]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Deep-sea thermophilic bacteriophage d6e]]		[[Category: Deep-sea thermophilic bacteriophage d6e]]
		+	[[Category: Large Structures]]
	[[Category: Antson, A A]]		[[Category: Antson, A A]]
	[[Category: Greive, S J]]		[[Category: Greive, S J]]

OCA at 07:44, 6 December 2017

OCA — Wed, 06 Dec 2017 07:44:32 GMT

←Older revision		Revision as of 07:44, 6 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5oe9 is ~~ON HOLD until Paper~~ Publication	+	==Structure of large terminase from the thermophilic bacteriophage D6E in complex with sulfate (Crystal form 2)==
		+	<StructureSection load='5oe9' size='340' side='right' caption='[[5oe9]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5oe9]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Deep-sea_thermophilic_bacteriophage_d6e Deep-sea thermophilic bacteriophage d6e]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OE9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OE9 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5oe8\|5oe8]]</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=5oe9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oe9 OCA], [http://pdbe.org/5oe9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oe9 RCSB], [http://www.ebi.ac.uk/pdbsum/5oe9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oe9 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of the large terminase from the Geobacillus stearothermophilus bacteriophage D6E shows a unique relative orientation of the N-terminal adenosine triphosphatase (ATPase) and C-terminal nuclease domains. This monomeric 'initiation' state with the two domains 'locked' together is stabilized via a conserved C-terminal arm, which may interact with the portal protein during motor assembly, as predicted for several bacteriophages. Further work supports the formation of an active oligomeric state: (i) AUC data demonstrate the presence of oligomers; (ii) mutational analysis reveals a trans -arginine finger, R158, indispensable for ATP hydrolysis; (iii) the location of this arginine is conserved with the HerA/FtsK ATPase superfamily; (iv) a molecular docking model of the pentamer is compatible with the location of the identified arginine finger. However, this pentameric model is structurally incompatible with the monomeric 'initiation' state and is supported by the observed increase in k cat of ATP hydrolysis, from 7.8 +/- 0.1 min -1 to 457.7 +/- 9.2 min -1 upon removal of the C-terminal nuclease domain. Taken together, these structural, biophysical and biochemical data suggest a model where transition from the 'initiation' state into a catalytically competent pentameric state, is accompanied by substantial domain rearrangements, triggered by the removal of the C-terminal arm from the ATPase active site.

-	~~Authors~~:	+	Structure of the large terminase from a hyperthermophilic virus reveals a unique mechanism for oligomerization and ATP hydrolysis.,Xu RG, Jenkins HT, Antson AA, Greive SJ Nucleic Acids Res. 2017 Oct 24. pii: 4563303. doi: 10.1093/nar/gkx947. PMID:29069443<ref>PMID:29069443</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5oe9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Deep-sea thermophilic bacteriophage d6e]]
		+	[[Category: Antson, A A]]
		+	[[Category: Greive, S J]]
		+	[[Category: Jenkins, H T]]
		+	[[Category: Xu, R G]]
		+	[[Category: Large terminase]]
		+	[[Category: Viral protein]]

OCA: Protected "5oe9" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 12:20:01 GMT

Protected "5oe9" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:20, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5oe9 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 12:20:00 GMT

New page: '''Unreleased structure''' The entry 5oe9 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5oe9 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]