5e5o - Revision history

OCA at 06:13, 5 July 2023

OCA — Wed, 05 Jul 2023 06:13:52 GMT

←Older revision		Revision as of 06:13, 5 July 2023
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	<StructureSection load='5e5o' size='340' side='right'caption='[[5e5o]], [[Resolution\|resolution]] 2.36Å' scene=''>		<StructureSection load='5e5o' size='340' side='right'caption='[[5e5o]], [[Resolution\|resolution]] 2.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e5o]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Sormk Sormk~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E5O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5E5O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e5o]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Sordaria_macrospora_k-hell Sordaria macrospora k-hell] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E5O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5E5O 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=EDO:1,~~2~~-ETHANEDIOL'>EDO</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]] 2.36Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[4lox\|4lox]], [[5e5p\|5e5p]], [[5e5s\|5e5s]], [[5e63\|5e63]], [[5e67\|5e67]]~~<~~/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=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">SMAC_12671 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=771870 SORMK])~~</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=5e5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e5o OCA], [https://pdbe.org/5e5o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5e5o RCSB], [https://www.ebi.ac.uk/pdbsum/5e5o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5e5o 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=5e5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e5o OCA], [~~http~~://pdbe.org/5e5o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5e5o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5e5o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5e5o ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/F7WD42_SORMK F7WD42_SORMK]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Sormk]]~~	+	[[Category: Sordaria macrospora k-hell]]
-	~~[[Category: Shen, B W]]~~	+	[[Category: Synthetic construct]]
-	~~[[Category: Complex]]~~	+	[[Category: Shen BW]]
-	~~[[Category: Hydrolase~~-~~dna complex~~]]	+
-	[[Category: ~~I-smami~~]]	+
-	[[Category: ~~Laglidadg]]~~	+
-	~~[[Category: Uncleaved~~]]	+

OCA at 11:30, 25 December 2019

OCA — Wed, 25 Dec 2019 11:30:30 GMT

←Older revision		Revision as of 11:30, 25 December 2019
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	==I-SmaMI bound to uncleaved DNA target in the presence of Calcium ions==		==I-SmaMI bound to uncleaved DNA target in the presence of Calcium ions==
-	<StructureSection load='5e5o' size='340' side='right' caption='[[5e5o]], [[Resolution\|resolution]] 2.36Å' scene=''>	+	<StructureSection load='5e5o' size='340' side='right'caption='[[5e5o]], [[Resolution\|resolution]] 2.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e5o]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E5O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5E5O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e5o]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sormk Sormk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E5O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5E5O 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=EDO:1,2-ETHANEDIOL'>EDO</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=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4lox\|4lox]], [[5e5p\|5e5p]], [[5e5s\|5e5s]], [[5e63\|5e63]], [[5e67\|5e67]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4lox\|4lox]], [[5e5p\|5e5p]], [[5e5s\|5e5s]], [[5e63\|5e63]], [[5e67\|5e67]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SMAC_12671 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=771870 SORMK])</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=5e5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e5o OCA], [http://pdbe.org/5e5o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e5o RCSB], [http://www.ebi.ac.uk/pdbsum/5e5o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e5o 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=5e5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e5o OCA], [http://pdbe.org/5e5o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e5o RCSB], [http://www.ebi.ac.uk/pdbsum/5e5o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e5o ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 5e5o" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5e5o" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Sormk]]
	[[Category: Shen, B W]]		[[Category: Shen, B W]]
	[[Category: Complex]]		[[Category: Complex]]

OCA at 06:44, 6 October 2017

OCA — Fri, 06 Oct 2017 06:44:12 GMT

←Older revision		Revision as of 06:44, 6 October 2017
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		+
	==I-SmaMI bound to uncleaved DNA target in the presence of Calcium ions==		==I-SmaMI bound to uncleaved DNA target in the presence of Calcium ions==
	<StructureSection load='5e5o' size='340' side='right' caption='[[5e5o]], [[Resolution\|resolution]] 2.36Å' scene=''>		<StructureSection load='5e5o' size='340' side='right' caption='[[5e5o]], [[Resolution\|resolution]] 2.36Å' scene=''>
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	</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=EDO:1,2-ETHANEDIOL'>EDO</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=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4lox\|4lox]], [[5e5p\|5e5p]], [[5e5s\|5e5s]], [[5e63\|5e63]], [[5e67\|5e67]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4lox\|4lox]], [[5e5p\|5e5p]], [[5e5s\|5e5s]], [[5e63\|5e63]], [[5e67\|5e67]]</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=5e5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e5o OCA], [http://pdbe.org/5e5o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e5o RCSB], [http://www.ebi.ac.uk/pdbsum/5e5o PDBsum]</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=5e5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e5o OCA], [http://pdbe.org/5e5o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e5o RCSB], [http://www.ebi.ac.uk/pdbsum/5e5o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e5o ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:15, 13 January 2016

OCA — Wed, 13 Jan 2016 20:15:36 GMT

←Older revision		Revision as of 20:15, 13 January 2016
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-	'''~~Unreleased~~ structure'''	+	==I-SmaMI bound to uncleaved DNA target in the presence of Calcium ions==
		+	<StructureSection load='5e5o' size='340' side='right' caption='[[5e5o]], [[Resolution\|resolution]] 2.36Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5e5o]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E5O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5E5O 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=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4lox\|4lox]], [[5e5p\|5e5p]], [[5e5s\|5e5s]], [[5e63\|5e63]], [[5e67\|5e67]]</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=5e5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e5o OCA], [http://pdbe.org/5e5o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e5o RCSB], [http://www.ebi.ac.uk/pdbsum/5e5o PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	LAGLIDADG homing endonucleases ("meganucleases") are highly specific DNA cleaving enzymes that are used for genome engineering. Like other enzymes that act on DNA targets, meganucleases often display binding affinities and cleavage activities that are dominated by one protein domain. To decipher the underlying mechanism of asymmetric DNA recognition and catalysis, we identified and characterized a new monomeric meganuclease (I-SmaMI), which belongs to a superfamily of homologous enzymes that recognize divergent DNA sequences. We solved a series of crystal structures of the enzyme-DNA complex representing a progression of sequential reaction states, and we compared the structural rearrangements and surface potential distributions within each protein domain against their relative contribution to binding affinity. We then determined the effects of equivalent point mutations in each of the two enzyme active sites to determine whether asymmetry in DNA recognition is translated into corresponding asymmetry in DNA cleavage activity. These experiments demonstrate the structural basis for "dominance" by one protein domain over the other and provide insights into this enzyme's conformational switch from a nonspecific search mode to a more specific recognition mode.

-	The ~~entry 5e5o is ON HOLD until Paper Publication~~	+	The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease.,Shen BW, Lambert A, Walker BC, Stoddard BL, Kaiser BK J Mol Biol. 2015 Dec 15. pii: S0022-2836(15)00696-8. doi:, 10.1016/j.jmb.2015.12.005. PMID:26705195<ref>PMID:26705195</ref>

-	~~Authors~~: Shen, B.W.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: I-~~SmaMI bound to uncleaved DNA target in the presence of Calcium ions~~	+	<div class="pdbe-citations 5e5o" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
-	[[Category: ~~Shen, B.W~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Shen, B W]]
		+	[[Category: Complex]]
		+	[[Category: Hydrolase-dna complex]]
		+	[[Category: I-smami]]
		+	[[Category: Laglidadg]]
		+	[[Category: Uncleaved]]

OCA at 09:34, 7 January 2016

OCA — Thu, 07 Jan 2016 09:34:16 GMT

←Older revision		Revision as of 09:34, 7 January 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5e5o is ON HOLD	+	The entry 5e5o is ON HOLD until Paper Publication

	Authors: Shen, B.W.		Authors: Shen, B.W.

OCA: Protected "5e5o" [edit=sysop:move=sysop]

OCA — Fri, 16 Oct 2015 03:02:30 GMT

Protected "5e5o" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:02, 16 October 2015

OCA: New page: '''Unreleased structure''' The entry 5e5o is ON HOLD Authors: Shen, B.W. Description: I-SmaMI bound to uncleaved DNA target in the presence of Calcium ions [[Category: Unreleased Struc...

OCA — Fri, 16 Oct 2015 03:02:28 GMT

New page: '''Unreleased structure''' The entry 5e5o is ON HOLD Authors: Shen, B.W. Description: I-SmaMI bound to uncleaved DNA target in the presence of Calcium ions [[Category: Unreleased Struc...

New page

'''Unreleased structure'''

The entry 5e5o is ON HOLD

Authors: Shen, B.W.

Description: I-SmaMI bound to uncleaved DNA target in the presence of Calcium ions
[[Category: Unreleased Structures]]
[[Category: Shen, B.W]]