3rtv - Revision history

OCA at 12:37, 14 March 2024

2024-03-14T12:37:16Z

←Older revision		Revision as of 12:37, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3rtv' size='340' side='right'caption='[[3rtv]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3rtv' size='340' side='right'caption='[[3rtv]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rtv]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_25104 Atcc 25104~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RTV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RTV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rtv]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RTV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RTV FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DCP:2~~-~~DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.9Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~DDG~~:~~2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE~~'>~~DDG~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class~~=~~"sblockDat"><div style~~=~~'overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[3ktq\|3ktq]]~~</~~div~~><~~/td></tr>~~	+
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">pol I~~, ~~pol1, polA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])~~<~~/td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7]~~ </~~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=3rtv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rtv OCA], [https://pdbe.org/3rtv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rtv RCSB], [https://www.ebi.ac.uk/pdbsum/3rtv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rtv 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=3rtv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rtv OCA], [https://pdbe.org/3rtv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rtv RCSB], [https://www.ebi.ac.uk/pdbsum/3rtv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rtv ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/DPO1_THEAQ DPO1_THEAQ]
-	Many candidate unnatural DNA base pairs have been developed, but some of the best-replicated pairs adopt intercalated structures in free DNA that are difficult to reconcile with known mechanisms of polymerase recognition. Here we present crystal structures of KlenTaq DNA polymerase at different stages of replication for one such pair, dNaM-d5SICS, and show that efficient replication results from the polymerase itself, inducing the required natural-like structure.	+

-	KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.,Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A Nat Chem Biol. 2012 Jun 3. doi: 10.1038/nchembio.966. PMID:22660438<ref>PMID:22660438</ref>	+	==See Also==
-		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 3rtv" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 25104]]
-	[[Category: DNA-directed DNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Betz, K~~]]	+	[[Category: Thermus aquaticus]]
-	[[Category: ~~Diederichs,~~ K]]	+	[[Category: Betz K]]
-	[[Category: ~~Marx, A~~]]	+	[[Category: Diederichs K]]
-	[[Category: ~~Dna polymerase]]~~	+	[[Category: Marx A]]
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 10:25, 22 June 2022

2022-06-22T10:25:05Z

←Older revision		Revision as of 10:25, 22 June 2022
Line 1:		Line 1:

	==Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with natural primer/template DNA==		==Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with natural primer/template DNA==
-	<StructureSection load='3rtv' size='340' side='right' caption='[[3rtv]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='3rtv' size='340' side='right'caption='[[3rtv]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rtv]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RTV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3RTV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rtv]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RTV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RTV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ktq\|3ktq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ktq\|3ktq]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol I, pol1, polA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol I, pol1, polA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=3rtv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rtv OCA], [~~http~~://pdbe.org/3rtv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3rtv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3rtv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3rtv 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=3rtv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rtv OCA], [https://pdbe.org/3rtv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rtv RCSB], [https://www.ebi.ac.uk/pdbsum/3rtv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rtv ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 3rtv" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3rtv" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
Line 29:		Line 26:
	[[Category: Atcc 25104]]		[[Category: Atcc 25104]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Betz, K]]		[[Category: Betz, K]]
	[[Category: Diederichs, K]]		[[Category: Diederichs, K]]

OCA at 16:30, 11 August 2016

2016-08-11T16:30:49Z

←Older revision		Revision as of 16:30, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with natural primer/template DNA==		==Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with natural primer/template DNA==
	<StructureSection load='3rtv' size='340' side='right' caption='[[3rtv]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3rtv' size='340' side='right' caption='[[3rtv]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rtv]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_aquaticus Thermus aquaticus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RTV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RTV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rtv]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RTV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RTV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ktq\|3ktq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ktq\|3ktq]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol I, pol1, polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ~~Thermus aquaticus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol I, pol1, polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=3rtv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rtv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rtv RCSB], [http://www.ebi.ac.uk/pdbsum/3rtv 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=3rtv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rtv OCA], [http://pdbe.org/3rtv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rtv RCSB], [http://www.ebi.ac.uk/pdbsum/3rtv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rtv ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 18:		Line 19:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3rtv" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 25:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 25104]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Thermus aquaticus]]
	[[Category: Betz, K]]		[[Category: Betz, K]]
	[[Category: Diederichs, K]]		[[Category: Diederichs, K]]

OCA at 09:54, 4 January 2015

2015-01-04T09:54:13Z

←Older revision		Revision as of 09:54, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3rtv]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RTV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RTV FirstGlance]. <br>		<table><tr><td colspan='2'>[[3rtv]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RTV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RTV FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ktq\|3ktq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ktq\|3ktq]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol I, pol1, polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol I, pol1, polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rtv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rtv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rtv RCSB], [http://www.ebi.ac.uk/pdbsum/3rtv 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=3rtv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rtv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rtv RCSB], [http://www.ebi.ac.uk/pdbsum/3rtv PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 16:		Line 16:
	KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.,Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A Nat Chem Biol. 2012 Jun 3. doi: 10.1038/nchembio.966. PMID:22660438<ref>PMID:22660438</ref>		KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.,Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A Nat Chem Biol. 2012 Jun 3. doi: 10.1038/nchembio.966. PMID:22660438<ref>PMID:22660438</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>

Line 27:		Line 27:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]
-	[[Category: Betz, K.]]	+	[[Category: Betz, K]]
-	[[Category: Diederichs, K.]]	+	[[Category: Diederichs, K]]
-	[[Category: Marx, A.]]	+	[[Category: Marx, A]]
	[[Category: Dna polymerase]]		[[Category: Dna polymerase]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 04:46, 5 June 2014

2014-06-05T04:46:31Z

←Older revision		Revision as of 04:46, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3rtv.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with natural primer/template DNA==
		+	<StructureSection load='3rtv' size='340' side='right' caption='[[3rtv]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3rtv]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RTV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RTV FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ktq\|3ktq]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol I, pol1, polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rtv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rtv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rtv RCSB], [http://www.ebi.ac.uk/pdbsum/3rtv PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many candidate unnatural DNA base pairs have been developed, but some of the best-replicated pairs adopt intercalated structures in free DNA that are difficult to reconcile with known mechanisms of polymerase recognition. Here we present crystal structures of KlenTaq DNA polymerase at different stages of replication for one such pair, dNaM-d5SICS, and show that efficient replication results from the polymerase itself, inducing the required natural-like structure.

-	~~{{STRUCTURE_3rtv\| PDB=3rtv \| SCENE= }}~~	+	KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.,Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A Nat Chem Biol. 2012 Jun 3. doi: 10.1038/nchembio.966. PMID:22660438<ref>PMID:22660438</ref>

-	~~===Crystal structure~~ of the ~~large fragment~~ of ~~DNA polymerase I from Thermus Aquaticus in a closed ternary complex with natural primer~~/~~template DNA===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_22660438}}~~	+	==See Also==
-		+	*[[DNA polymerase\|DNA polymerase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~3rtv~~]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RTV OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:022660438<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]

OCA at 06:54, 4 July 2012

2012-07-04T06:54:05Z

←Older revision		Revision as of 06:54, 4 July 2012
Line 1:		Line 1:
	[[Image:3rtv.png\|left\|200px]]		[[Image:3rtv.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3rtv", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3rtv\| PDB=3rtv \| SCENE= }}		{{STRUCTURE_3rtv\| PDB=3rtv \| SCENE= }}

	===Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with natural primer/template DNA===		===Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with natural primer/template DNA===

		+	{{ABSTRACT_PUBMED_22660438}}

	==About this Structure==		==About this Structure==
	[[3rtv]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RTV OCA].		[[3rtv]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RTV OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022660438</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]

OCA at 06:57, 6 June 2012

2012-06-06T06:57:03Z

←Older revision		Revision as of 06:57, 6 June 2012
Line 1:		Line 1:
-	[[Image:3rtv.~~jpg~~\|left\|200px]]	+	[[Image:3rtv.png\|left\|200px]]

	<!--		<!--

OCA at 05:59, 30 May 2012

2012-05-30T05:59:03Z

←Older revision		Revision as of 05:59, 30 May 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3rtv.jpg\|left\|200px]]

-	The ~~entry 3rtv~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3rtv", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3rtv\| PDB=3rtv \| SCENE= }}

-	~~Authors: Marx, A., Diederichs, K., Betz, K.~~	+	===Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with natural primer/template DNA===

-	~~Description: Crystal~~ structure ~~of the large fragment of DNA polymerase I~~ from Thermus ~~Aquaticus in a closed ternary complex with natural primer~~/~~template~~ DNA	+
		+	==About this Structure==
		+	[[3rtv]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RTV OCA].
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Thermus aquaticus]]
		+	[[Category: Betz, K.]]
		+	[[Category: Diederichs, K.]]
		+	[[Category: Marx, A.]]
		+	[[Category: Dna polymerase]]
		+	[[Category: Transferase-dna complex]]

OCA at 05:23, 1 June 2011

2011-06-01T05:23:33Z

←Older revision		Revision as of 05:23, 1 June 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3rtv is ON HOLD	+	The entry 3rtv is ON HOLD until Paper Publication

	Authors: Marx, A., Diederichs, K., Betz, K.		Authors: Marx, A., Diederichs, K., Betz, K.

	Description: Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with natural primer/template DNA		Description: Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with natural primer/template DNA

OCA: Protected "3rtv" [edit=sysop:move=sysop]

2011-05-12T04:24:38Z

Protected "3rtv" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:24, 12 May 2011