4yit - Revision history

OCA at 08:01, 27 September 2023

OCA — Wed, 27 Sep 2023 08:01:16 GMT

←Older revision		Revision as of 08:01, 27 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4yit]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Gremmeniella_abietina Gremmeniella abietina] 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=4YIT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YIT FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yit]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Gremmeniella_abietina Gremmeniella abietina] 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=4YIT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YIT FirstGlance]. <br>
-	</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></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]] 3.24Å</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></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=4yit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yit OCA], [https://pdbe.org/4yit PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yit RCSB], [https://www.ebi.ac.uk/pdbsum/4yit PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yit 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=4yit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yit OCA], [https://pdbe.org/4yit PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yit RCSB], [https://www.ebi.ac.uk/pdbsum/4yit PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yit ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:15, 3 May 2023

OCA — Wed, 03 May 2023 08:15:35 GMT

←Older revision		Revision as of 08:15, 3 May 2023
Line 3:		Line 3:
	<StructureSection load='4yit' size='340' side='right'caption='[[4yit]], [[Resolution\|resolution]] 3.24Å' scene=''>		<StructureSection load='4yit' size='340' side='right'caption='[[4yit]], [[Resolution\|resolution]] 3.24Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yit]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ascocalyx_abietina Ascocalyx~~ abietina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YIT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YIT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yit]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Gremmeniella_abietina Gremmeniella abietina] 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=4YIT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YIT 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>~~</td></tr>~~	+	</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></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yis\|4yis]]~~</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=4yit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yit OCA], [https://pdbe.org/4yit PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yit RCSB], [https://www.ebi.ac.uk/pdbsum/4yit PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yit 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=4yit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yit OCA], [~~http~~://pdbe.org/4yit PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4yit RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4yit PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4yit ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A158RFF2_9HELO A0A158RFF2_9HELO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ascocalyx~~ abietina]]	+	[[Category: Gremmeniella abietina]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Hallinan, J P~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Stoddard, B L~~]]	+	[[Category: Hallinan JP]]
-	[[Category: ~~Homing endonuclease]]~~	+	[[Category: Stoddard BL]]
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Laglidadg]]~~	+
-	~~[[Category: Meganuclease~~]]	+

OCA at 10:50, 25 December 2019

OCA — Wed, 25 Dec 2019 10:50:13 GMT

←Older revision		Revision as of 10:50, 25 December 2019
Line 1:		Line 1:

	==Crystal Structure of LAGLIDADG Meganuclease I-AabMI Bound to Uncleaved DNA==		==Crystal Structure of LAGLIDADG Meganuclease I-AabMI Bound to Uncleaved DNA==
-	<StructureSection load='4yit' size='340' side='right' caption='[[4yit]], [[Resolution\|resolution]] 3.24Å' scene=''>	+	<StructureSection load='4yit' size='340' side='right'caption='[[4yit]], [[Resolution\|resolution]] 3.24Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4yit]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Ascocalyx_abietina Ascocalyx abietina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YIT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YIT FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yit]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Ascocalyx_abietina Ascocalyx abietina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YIT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YIT FirstGlance]. <br>
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Ascocalyx abietina]]		[[Category: Ascocalyx abietina]]
		+	[[Category: Large Structures]]
	[[Category: Hallinan, J P]]		[[Category: Hallinan, J P]]
	[[Category: Stoddard, B L]]		[[Category: Stoddard, B L]]

OCA at 15:49, 15 November 2017

OCA — Wed, 15 Nov 2017 15:49:12 GMT

←Older revision		Revision as of 15:49, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='4yit' size='340' side='right' caption='[[4yit]], [[Resolution\|resolution]] 3.24Å' scene=''>		<StructureSection load='4yit' size='340' side='right' caption='[[4yit]], [[Resolution\|resolution]] 3.24Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yit]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YIT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YIT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yit]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Ascocalyx_abietina Ascocalyx abietina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YIT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YIT 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></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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yis\|4yis]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yis\|4yis]]</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=4yit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yit OCA], [http://pdbe.org/4yit PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yit RCSB], [http://www.ebi.ac.uk/pdbsum/4yit 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=4yit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yit OCA], [http://pdbe.org/4yit PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yit RCSB], [http://www.ebi.ac.uk/pdbsum/4yit PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yit ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ascocalyx abietina]]
	[[Category: Hallinan, J P]]		[[Category: Hallinan, J P]]
	[[Category: Stoddard, B L]]		[[Category: Stoddard, B L]]

OCA at 07:42, 1 June 2016

OCA — Wed, 01 Jun 2016 07:42:50 GMT

←Older revision		Revision as of 07:42, 1 June 2016
Line 8:		Line 8:
	<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=4yit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yit OCA], [http://pdbe.org/4yit PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yit RCSB], [http://www.ebi.ac.uk/pdbsum/4yit 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=4yit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yit OCA], [http://pdbe.org/4yit PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yit RCSB], [http://www.ebi.ac.uk/pdbsum/4yit PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	LAGLIDADG meganucleases are DNA cleaving enzymes used for genome engineering. While their cleavage specificity can be altered using several protein engineering and selection strategies, their overall targetability is limited by highly specific indirect recognition of the central four base pairs within their recognition sites. In order to examine the physical basis of indirect sequence recognition and to expand the number of such nucleases available for genome engineering, we have determined the target sites, DNA-bound structures, and central four cleavage fidelities of nine related enzymes. Subsequent crystallographic analyses of a meganuclease bound to two noncleavable target sites, each containing a single inactivating base pair substitution at its center, indicates that a localized slip of the mutated base pair causes a small change in the DNA backbone conformation that results in a loss of metal occupancy at one binding site, eliminating cleavage activity.
		+
		+	Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity.,Lambert AR, Hallinan JP, Shen BW, Chik JK, Bolduc JM, Kulshina N, Robins LI, Kaiser BK, Jarjour J, Havens K, Scharenberg AM, Stoddard BL Structure. 2016 Apr 27. pii: S0969-2126(16)30035-1. doi:, 10.1016/j.str.2016.03.024. PMID:27133026<ref>PMID:27133026</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4yit" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:59, 10 May 2016

OCA — Tue, 10 May 2016 17:59:50 GMT

←Older revision		Revision as of 17:59, 10 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 4yit ~~is ON HOLD until Paper Publication~~	+	==Crystal Structure of LAGLIDADG Meganuclease I-AabMI Bound to Uncleaved DNA==
-		+	<StructureSection load='4yit' size='340' side='right' caption='[[4yit]], [[Resolution\|resolution]] 3.24Å' scene=''>
-	~~Authors~~: ~~Hallinan, J~~.P.~~, Stoddard, B~~.L.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4yit]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YIT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YIT FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yis\|4yis]]</td></tr>
-	[[Category: Hallinan, J.P]]	+	<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=4yit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yit OCA], [http://pdbe.org/4yit PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yit RCSB], [http://www.ebi.ac.uk/pdbsum/4yit PDBsum]</span></td></tr>
-	[[Category: Stoddard, B.L]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hallinan, J P]]
		+	[[Category: Stoddard, B L]]
		+	[[Category: Homing endonuclease]]
		+	[[Category: Hydrolase-dna complex]]
		+	[[Category: Laglidadg]]
		+	[[Category: Meganuclease]]

OCA at 11:34, 1 April 2015

OCA — Wed, 01 Apr 2015 11:34:19 GMT

←Older revision		Revision as of 11:34, 1 April 2015
Line 5:		Line 5:
	Authors: Hallinan, J.P., Stoddard, B.L.		Authors: Hallinan, J.P., Stoddard, B.L.

-	Description: ~~Crystal Structure of LAGLIDADG Meganuclease I-AabMI Bound to Uncleaved DNA~~	+	Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Hallinan, J.P]]		[[Category: Hallinan, J.P]]
	[[Category: Stoddard, B.L]]		[[Category: Stoddard, B.L]]

OCA at 12:28, 26 March 2015

OCA — Thu, 26 Mar 2015 12:28:35 GMT

←Older revision		Revision as of 12:28, 26 March 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4yit is ON HOLD	+	The entry 4yit is ON HOLD until Paper Publication

-	Authors: Hallinan, J.P.	+	Authors: Hallinan, J.P., Stoddard, B.L.

	Description: Crystal Structure of LAGLIDADG Meganuclease I-AabMI Bound to Uncleaved DNA		Description: Crystal Structure of LAGLIDADG Meganuclease I-AabMI Bound to Uncleaved DNA
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Hallinan, J.P]]		[[Category: Hallinan, J.P]]
		+	[[Category: Stoddard, B.L]]

OCA: Protected "4yit" [edit=sysop:move=sysop]

OCA — Wed, 11 Mar 2015 10:41:32 GMT

Protected "4yit" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:41, 11 March 2015

OCA: New page: '''Unreleased structure''' The entry 4yit is ON HOLD Authors: Hallinan, J.P. Description: Crystal Structure of LAGLIDADG Meganuclease I-AabMI Bound to Uncleaved DNA [[Category: Unrelea...

OCA — Wed, 11 Mar 2015 10:41:31 GMT

New page: '''Unreleased structure''' The entry 4yit is ON HOLD Authors: Hallinan, J.P. Description: Crystal Structure of LAGLIDADG Meganuclease I-AabMI Bound to Uncleaved DNA [[Category: Unrelea...

New page

'''Unreleased structure'''

The entry 4yit is ON HOLD

Authors: Hallinan, J.P.

Description: Crystal Structure of LAGLIDADG Meganuclease I-AabMI Bound to Uncleaved DNA
[[Category: Unreleased Structures]]
[[Category: Hallinan, J.P]]