1t3w - Revision history

OCA at 08:38, 1 May 2024

2024-05-01T08:38:09Z

←Older revision		Revision as of 08:38, 1 May 2024
Line 3:		Line 3:
	<StructureSection load='1t3w' size='340' side='right'caption='[[1t3w]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1t3w' size='340' side='right'caption='[[1t3w]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t3w]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1T3W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t3w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T3W FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACY:ACETIC+ACID'>ACY</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]] 2.8Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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;~~'>~~[[1dd9\|1dd9]]~~</~~div~~>~~</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=1t3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3w OCA], [https://pdbe.org/1t3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t3w RCSB], [https://www.ebi.ac.uk/pdbsum/1t3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t3w ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaG, dnaP, parB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1t3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3w OCA], [~~http~~://pdbe.org/1t3w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1t3w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1t3w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1t3w ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~PRIM_ECOLI PRIM_ECOLI~~]~~] DNA primase is the~~ polymerase that ~~synthesizes small~~ RNA primers for ~~the Okazaki fragments on both template strands at replication forks~~ during ~~chromosomal~~ DNA ~~synthesis~~.	+	[https://www.uniprot.org/uniprot/DNAG_ECOLI DNAG_ECOLI] RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication.[HAMAP-Rule:MF_00974]<ref>PMID:1511009</ref> <ref>PMID:340457</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 22:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1t3w ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1t3w ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	During bacterial DNA replication, the DnaG primase interacts with the hexameric DnaB helicase to synthesize RNA primers for extension by DNA polymerase. In Escherichia coli, this occurs by transient interaction of primase with the helicase. Here we demonstrate directly by surface plasmon resonance that the C-terminal domain of primase is responsible for interaction with DnaB6. Determination of the 2.8-angstroms crystal structure of the C-terminal domain of primase revealed an asymmetric dimer. The monomers have an N-terminal helix bundle similar to the N-terminal domain of DnaB, followed by a long helix that connects to a C-terminal helix hairpin. The connecting helix is interrupted differently in the two monomers. Solution studies using NMR showed that an equilibrium exists between a monomeric species with an intact, extended but naked, connecting helix and a dimer in which this helix is interrupted in the same way as in one of the crystal conformers. The other conformer is not significantly populated in solution, and its presence in the crystal is due largely to crystal packing forces. It is proposed that the connecting helix contributes necessary structural flexibility in the primase-helicase complex at replication forks.
-
-	Crystal and solution structures of the helicase-binding domain of Escherichia coli primase.,Oakley AJ, Loscha KV, Schaeffer PM, Liepinsh E, Pintacuda G, Wilce MC, Otting G, Dixon NE J Biol Chem. 2005 Mar 25;280(12):11495-504. Epub 2005 Jan 12. PMID:15649896<ref>PMID:15649896</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1t3w" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 38:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dixon~~, N E~~]]	+	[[Category: Dixon NE]]
-	[[Category: Liepinsh, E]]	+	[[Category: Liepinsh E]]
-	[[Category: Loscha~~, K V~~]]	+	[[Category: Loscha KV]]
-	[[Category: Oakley~~, A J~~]]	+	[[Category: Oakley AJ]]
-	[[Category: Otting, G]]	+	[[Category: Otting G]]
-	[[Category: Schaeffer~~, P M~~]]	+	[[Category: Schaeffer PM]]
-	[[Category: Wilce~~, M C.J]]~~	+	[[Category: Wilce MCJ]]
-	~~[[Category: Dna replication]]~~	+
-	~~[[Category: Dna-directed rna polymerase]]~~	+
-	~~[[Category: Dnag]]~~	+
-	~~[[Category: E. coli]]~~	+
-	~~[[Category: Replication~~]]	+

OCA at 11:41, 24 December 2020

2020-12-24T11:41:35Z

←Older revision		Revision as of 11:41, 24 December 2020
Line 1:		Line 1:

	==Crystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581)==		==Crystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581)==
-	<StructureSection load='1t3w' size='340' side='right' caption='[[1t3w]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='1t3w' size='340' side='right'caption='[[1t3w]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t3w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3W OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1T3W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t3w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3W OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1T3W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dd9\|1dd9]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dd9\|1dd9]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaG, dnaP, parB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaG, dnaP, parB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1t3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3w OCA], [http://pdbe.org/1t3w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t3w RCSB], [http://www.ebi.ac.uk/pdbsum/1t3w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t3w 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=1t3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3w OCA], [http://pdbe.org/1t3w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t3w RCSB], [http://www.ebi.ac.uk/pdbsum/1t3w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t3w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 33:		Line 33:

	==See Also==		==See Also==
-	*[[RNA polymerase\|RNA polymerase]]	+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Dixon, N E]]		[[Category: Dixon, N E]]
	[[Category: Liepinsh, E]]		[[Category: Liepinsh, E]]

OCA at 07:18, 11 July 2018

2018-07-11T07:18:14Z

←Older revision		Revision as of 07:18, 11 July 2018
Line 16:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t3/1t3w_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t3/1t3w_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 09:28, 3 October 2016

2016-10-03T09:28:28Z

←Older revision		Revision as of 09:28, 3 October 2016
Line 1:		Line 1:
		+
	==Crystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581)==		==Crystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581)==
	<StructureSection load='1t3w' size='340' side='right' caption='[[1t3w]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1t3w' size='340' side='right' caption='[[1t3w]], [[Resolution\|resolution]] 2.80Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dd9\|1dd9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dd9\|1dd9]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaG, dnaP, parB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaG, dnaP, parB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1t3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3w OCA], [http://pdbe.org/1t3w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t3w RCSB], [http://www.ebi.ac.uk/pdbsum/1t3w 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=1t3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3w OCA], [http://pdbe.org/1t3w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t3w RCSB], [http://www.ebi.ac.uk/pdbsum/1t3w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t3w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1t3w ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:39, 11 September 2015

2015-09-11T22:39:54Z

←Older revision		Revision as of 22:39, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1t3w' size='340' side='right' caption='[[1t3w]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1t3w' size='340' side='right' caption='[[1t3w]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t3w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T3W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t3w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T3W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dd9\|1dd9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dd9\|1dd9]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaG, dnaP, parB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaG, dnaP, parB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1t3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t3w RCSB], [http://www.ebi.ac.uk/pdbsum/1t3w 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=1t3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3w OCA], [http://pdbe.org/1t3w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t3w RCSB], [http://www.ebi.ac.uk/pdbsum/1t3w PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 1t3w" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Dixon, N E]]		[[Category: Dixon, N E]]
	[[Category: Liepinsh, E]]		[[Category: Liepinsh, E]]

OCA at 20:23, 25 December 2014

2014-12-25T20:23:51Z

←Older revision		Revision as of 20:23, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1t3w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T3W FirstGlance]. <br>		<table><tr><td colspan='2'>[[1t3w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T3W FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dd9\|1dd9]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dd9\|1dd9]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaG, dnaP, parB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaG, dnaP, parB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=1t3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t3w RCSB], [http://www.ebi.ac.uk/pdbsum/1t3w 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=1t3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t3w RCSB], [http://www.ebi.ac.uk/pdbsum/1t3w PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PRIM_ECOLI PRIM_ECOLI]] DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments on both template strands at replication forks during chromosomal DNA synthesis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Dixon, N E.]]	+	[[Category: Dixon, N E]]
-	[[Category: Liepinsh, E.]]	+	[[Category: Liepinsh, E]]
-	[[Category: Loscha, K V.]]	+	[[Category: Loscha, K V]]
-	[[Category: Oakley, A J.]]	+	[[Category: Oakley, A J]]
-	[[Category: Otting, G.]]	+	[[Category: Otting, G]]
-	[[Category: Schaeffer, P M.]]	+	[[Category: Schaeffer, P M]]
-	[[Category: Wilce, M C.J.]]	+	[[Category: Wilce, M C.J]]
	[[Category: Dna replication]]		[[Category: Dna replication]]
	[[Category: Dna-directed rna polymerase]]		[[Category: Dna-directed rna polymerase]]

OCA at 21:23, 28 September 2014

2014-09-28T21:23:10Z

←Older revision		Revision as of 21:23, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1t3w.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581)==
		+	<StructureSection load='1t3w' size='340' side='right' caption='[[1t3w]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1t3w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T3W FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dd9\|1dd9]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaG, dnaP, parB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=1t3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t3w RCSB], [http://www.ebi.ac.uk/pdbsum/1t3w PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t3/1t3w_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	During bacterial DNA replication, the DnaG primase interacts with the hexameric DnaB helicase to synthesize RNA primers for extension by DNA polymerase. In Escherichia coli, this occurs by transient interaction of primase with the helicase. Here we demonstrate directly by surface plasmon resonance that the C-terminal domain of primase is responsible for interaction with DnaB6. Determination of the 2.8-angstroms crystal structure of the C-terminal domain of primase revealed an asymmetric dimer. The monomers have an N-terminal helix bundle similar to the N-terminal domain of DnaB, followed by a long helix that connects to a C-terminal helix hairpin. The connecting helix is interrupted differently in the two monomers. Solution studies using NMR showed that an equilibrium exists between a monomeric species with an intact, extended but naked, connecting helix and a dimer in which this helix is interrupted in the same way as in one of the crystal conformers. The other conformer is not significantly populated in solution, and its presence in the crystal is due largely to crystal packing forces. It is proposed that the connecting helix contributes necessary structural flexibility in the primase-helicase complex at replication forks.

-	~~{{STRUCTURE_1t3w\| PDB=1t3w \| SCENE= }}~~	+	Crystal and solution structures of the helicase-binding domain of Escherichia coli primase.,Oakley AJ, Loscha KV, Schaeffer PM, Liepinsh E, Pintacuda G, Wilce MC, Otting G, Dixon NE J Biol Chem. 2005 Mar 25;280(12):11495-504. Epub 2005 Jan 12. PMID:15649896<ref>PMID:15649896</ref>

-	~~===Crystal Structure~~ of the E.~~coli DnaG C-terminal domain (residues 434 to 581)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15649896}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1t3w]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3W OCA].~~	+

	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015649896<~~/~~ref~~><~~ref group="xtra">PMID:014711519</ref><references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Dixon, N E.]]		[[Category: Dixon, N E.]]

OCA at 21:04, 20 October 2012

2012-10-20T21:04:31Z

←Older revision		Revision as of 21:04, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1t3w]] is a 2 chain structure ~~of [[RNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3W OCA].	+	[[1t3w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3W OCA].

	==See Also==		==See Also==

OCA at 12:31, 27 July 2012

2012-07-27T12:31:07Z

←Older revision		Revision as of 12:31, 27 July 2012
Line 1:		Line 1:
	[[Image:1t3w.png\|left\|200px]]		[[Image:1t3w.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1t3w", 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_1t3w\| PDB=1t3w \| SCENE= }}		{{STRUCTURE_1t3w\| PDB=1t3w \| SCENE= }}

	===Crystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581)===		===Crystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15649896}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15649896 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15649896}}		{{ABSTRACT_PUBMED_15649896}}

	==About this Structure==		==About this Structure==
-	[[1t3w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3W OCA].	+	[[1t3w]] is a 2 chain structure of [[RNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3W OCA].
		+
		+	==See Also==
		+	*[[RNA polymerase\|RNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15649896~~</ref><ref group="xtra">PMID:~~14711519~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015649896</ref><ref group="xtra">PMID:014711519</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Dixon, N E.]]		[[Category: Dixon, N E.]]
Line 35:		Line 27:
	[[Category: Dnag]]		[[Category: Dnag]]
	[[Category: E. coli]]		[[Category: E. coli]]
		+	[[Category: Replication]]

OCA: Protected "1t3w" [edit=sysop:move=sysop]

2011-03-14T22:54:32Z

Protected "1t3w" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:54, 14 March 2011