5o6g - Revision history

OCA at 19:09, 29 November 2023

OCA — Wed, 29 Nov 2023 19:09:46 GMT

←Older revision		Revision as of 19:09, 29 November 2023
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	<StructureSection load='5o6g' size='340' side='right'caption='[[5o6g]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='5o6g' size='340' side='right'caption='[[5o6g]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o6g]] is a 9 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_35582_[[desulfurococcus_mobilis~~]~~] Atcc 35582 [~~[~~desulfurococcus mobilis]]~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O6G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5O6G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o6g]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfurococcus_mucosus Desulfurococcus mucosus] 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=5O6G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O6G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.75Å</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=5o6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o6g OCA], [~~http~~://pdbe.org/5o6g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5o6g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5o6g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5o6g ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=5o6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o6g OCA], [https://pdbe.org/5o6g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o6g RCSB], [https://www.ebi.ac.uk/pdbsum/5o6g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o6g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DMO1_DESMO DMO1_DESMO]] Endonuclease involved in intron homing. Recognizes a recognizes up to 20 bp of DNA in the 23S rRNA gene intron. It has a slow turnover rate and cuts the coding strand with a slight preference over the non-coding strand.	+	[https://www.uniprot.org/uniprot/DMO1_DESMO DMO1_DESMO] Endonuclease involved in intron homing. Recognizes a recognizes up to 20 bp of DNA in the 23S rRNA gene intron. It has a slow turnover rate and cuts the coding strand with a slight preference over the non-coding strand.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Desulfurococcus mucosus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Marcaida, M J~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Molina, R~~]]	+	[[Category: Marcaida MJ]]
-	[[Category: ~~Desulfurococcus mobili]]~~	+	[[Category: Molina R]]
-	~~[[Category: Dna binding protein~~]]	+

OCA at 06:52, 16 October 2019

OCA — Wed, 16 Oct 2019 06:52:16 GMT

←Older revision		Revision as of 06:52, 16 October 2019
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	==Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI==		==Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI==
-	<StructureSection load='5o6g' size='340' side='right' caption='[[5o6g]], [[Resolution\|resolution]] 2.75Å' scene=''>	+	<StructureSection load='5o6g' size='340' side='right'caption='[[5o6g]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5o6g]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_35582_[[desulfurococcus_mobilis]] Atcc 35582 [[desulfurococcus mobilis]]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O6G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O6G FirstGlance]. <br>		<table><tr><td colspan='2'>[[5o6g]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_35582_[[desulfurococcus_mobilis]] Atcc 35582 [[desulfurococcus mobilis]]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O6G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O6G FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 5o6g" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5o6g" 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: Marcaida, M J]]		[[Category: Marcaida, M J]]
	[[Category: Molina, R]]		[[Category: Molina, R]]
	[[Category: Desulfurococcus mobili]]		[[Category: Desulfurococcus mobili]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]

OCA at 05:57, 3 January 2018

OCA — Wed, 03 Jan 2018 05:57:28 GMT

←Older revision		Revision as of 05:57, 3 January 2018
Line 3:		Line 3:
	<StructureSection load='5o6g' size='340' side='right' caption='[[5o6g]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='5o6g' size='340' side='right' caption='[[5o6g]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o6g]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O6G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O6G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o6g]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_35582_[[desulfurococcus_mobilis]] Atcc 35582 [[desulfurococcus mobilis]]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O6G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O6G FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=5o6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o6g OCA], [http://pdbe.org/5o6g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o6g RCSB], [http://www.ebi.ac.uk/pdbsum/5o6g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o6g 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=5o6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o6g OCA], [http://pdbe.org/5o6g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o6g RCSB], [http://www.ebi.ac.uk/pdbsum/5o6g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o6g ProSAT]</span></td></tr>

OCA at 07:11, 6 December 2017

OCA — Wed, 06 Dec 2017 07:11:38 GMT

←Older revision		Revision as of 07:11, 6 December 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5o6g is ~~ON HOLD~~	+	==Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI==
		+	<StructureSection load='5o6g' size='340' side='right' caption='[[5o6g]], [[Resolution\|resolution]] 2.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5o6g]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O6G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O6G FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=5o6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o6g OCA], [http://pdbe.org/5o6g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o6g RCSB], [http://www.ebi.ac.uk/pdbsum/5o6g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o6g ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DMO1_DESMO DMO1_DESMO]] Endonuclease involved in intron homing. Recognizes a recognizes up to 20 bp of DNA in the 23S rRNA gene intron. It has a slow turnover rate and cuts the coding strand with a slight preference over the non-coding strand.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	I-DmoI, from the hyperthermophilic archaeon Desulfurococcus mobilis, belongs to the LAGLIDADG homing endonuclease protein family. Its members are highly specific enzymes capable of recognizing long DNA target sequences, thus providing potential tools for genome manipulation. Working towards this particular application, many efforts have been made to generate mesophilic variants of I-DmoI that function at lower temperatures than the wild-type. Here, we report a structural and computational analysis of two I-DmoI mesophilic mutants. Despite very limited structural variations between the crystal structures of these variants and the wild-type, a different dynamical behaviour near the cleavage sites is observed. In particular, both the dynamics of the water molecules and the protein perturbation effect on the cleavage site correlate well with the changes observed in the experimental enzymatic activity.

-	~~Authors: Molina, R~~., Marcaida, M.J.	+	Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI.,Alba J, Marcaida MJ, Prieto J, Montoya G, Molina R, D'Abramo M J Comput Aided Mol Des. 2017 Nov 25. pii: 10.1007/s10822-017-0087-5. doi:, 10.1007/s10822-017-0087-5. PMID:29177929<ref>PMID:29177929</ref>

-	~~Description: Structures and dynamics~~ of ~~mesophilic variants from~~ the ~~homing endonuclease I~~-~~DmoI~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5o6g" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Marcaida, M J]]
	[[Category: Molina, R]]		[[Category: Molina, R]]
-	[[Category: ~~Marcaida, M.J~~]]	+	[[Category: Desulfurococcus mobili]]
		+	[[Category: Dna binding protein]]

OCA: Protected "5o6g" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 12:04:48 GMT

Protected "5o6g" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:04, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5o6g is ON HOLD Authors: Molina, R., Marcaida, M.J. Description: Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI...

OCA — Wed, 27 Sep 2017 12:04:47 GMT

New page: '''Unreleased structure''' The entry 5o6g is ON HOLD Authors: Molina, R., Marcaida, M.J. Description: Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI...

New page

'''Unreleased structure'''

The entry 5o6g is ON HOLD

Authors: Molina, R., Marcaida, M.J.

Description: Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI
[[Category: Unreleased Structures]]
[[Category: Molina, R]]
[[Category: Marcaida, M.J]]