3fyd - Revision history

OCA at 06:53, 6 September 2023

OCA — Wed, 06 Sep 2023 06:53:53 GMT

←Older revision		Revision as of 06:53, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3fyd' size='340' side='right'caption='[[3fyd]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='3fyd' size='340' side='right'caption='[[3fyd]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fyd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_43067 Atcc 43067~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FYD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fyd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FYD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.75Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]]~~<~~/div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">ksgA, MJ1029 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])~~</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=3fyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyd OCA], [https://pdbe.org/3fyd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fyd RCSB], [https://www.ebi.ac.uk/pdbsum/3fyd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fyd 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=3fyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyd OCA], [https://pdbe.org/3fyd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fyd RCSB], [https://www.ebi.ac.uk/pdbsum/3fyd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fyd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RSMA_METJA RSMA_METJA]] Specifically dimethylates two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits.[HAMAP-Rule:MF_00607]<ref>PMID:19520088</ref> <ref>PMID:20163168</ref>	+	[https://www.uniprot.org/uniprot/RSMA_METJA RSMA_METJA] Specifically dimethylates two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits.[HAMAP-Rule:MF_00607]<ref>PMID:19520088</ref> <ref>PMID:20163168</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43067]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Musayev, F N~~]]	+	[[Category: Methanocaldococcus jannaschii]]
-	[[Category: ~~Rife, J P~~]]	+	[[Category: Musayev FN]]
-	[[Category: ~~Scarsdale, J N~~]]	+	[[Category: Rife JP]]
-	[[Category: ~~Dimethyladenosine transferase]]~~	+	[[Category: Scarsdale JN]]
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Ribosomal assembly]]~~	+
-	~~[[Category: Rna-binding]]~~	+
-	~~[[Category: Rossmann fold]]~~	+
-	~~[[Category: Rrna methylase]]~~	+
-	~~[[Category: Rrna processing]]~~	+
-	~~[[Category: S-adenosyl-l-methionine]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 19:59, 20 October 2021

OCA — Wed, 20 Oct 2021 19:59:43 GMT

←Older revision		Revision as of 19:59, 20 October 2021
Line 1:		Line 1:

	==Crystal Structure of Dim1 from the thermophilic archeon, Methanocaldococcus jannaschi==		==Crystal Structure of Dim1 from the thermophilic archeon, Methanocaldococcus jannaschi==
-	<StructureSection load='3fyd' size='340' side='right' caption='[[3fyd]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='3fyd' size='340' side='right'caption='[[3fyd]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fyd]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3FYD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fyd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FYD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA, MJ1029 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA, MJ1029 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=3fyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyd OCA], [~~http~~://pdbe.org/3fyd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3fyd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3fyd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3fyd 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=3fyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyd OCA], [https://pdbe.org/3fyd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fyd RCSB], [https://www.ebi.ac.uk/pdbsum/3fyd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fyd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RSMA_METJA RSMA_METJA]] Specifically dimethylates two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits.[HAMAP-Rule:MF_00607]<ref>PMID:19520088</ref> <ref>PMID:20163168</ref>	+	[[https://www.uniprot.org/uniprot/RSMA_METJA RSMA_METJA]] Specifically dimethylates two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits.[HAMAP-Rule:MF_00607]<ref>PMID:19520088</ref> <ref>PMID:20163168</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 43067]]		[[Category: Atcc 43067]]
		+	[[Category: Large Structures]]
	[[Category: Musayev, F N]]		[[Category: Musayev, F N]]
	[[Category: Rife, J P]]		[[Category: Rife, J P]]

OCA at 07:25, 5 December 2018

OCA — Wed, 05 Dec 2018 07:25:44 GMT

←Older revision		Revision as of 07:25, 5 December 2018
Line 1:		Line 1:
		+
	==Crystal Structure of Dim1 from the thermophilic archeon, Methanocaldococcus jannaschi==		==Crystal Structure of Dim1 from the thermophilic archeon, Methanocaldococcus jannaschi==
	<StructureSection load='3fyd' size='340' side='right' caption='[[3fyd]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='3fyd' size='340' side='right' caption='[[3fyd]], [[Resolution\|resolution]] 1.75Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA, MJ1029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA, MJ1029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=3fyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyd OCA], [http://pdbe.org/3fyd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fyd RCSB], [http://www.ebi.ac.uk/pdbsum/3fyd 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=3fyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyd OCA], [http://pdbe.org/3fyd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fyd RCSB], [http://www.ebi.ac.uk/pdbsum/3fyd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fyd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fy/3fyd_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fy/3fyd_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 18:03, 8 February 2016

OCA — Mon, 08 Feb 2016 18:03:19 GMT

←Older revision		Revision as of 18:03, 8 February 2016
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA, MJ1029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA, MJ1029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=3fyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fyd RCSB], [http://www.ebi.ac.uk/pdbsum/3fyd 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=3fyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyd OCA], [http://pdbe.org/3fyd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fyd RCSB], [http://www.ebi.ac.uk/pdbsum/3fyd PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<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=3fyd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 28:
	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 3fyd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 01:11, 25 December 2014

OCA — Thu, 25 Dec 2014 01:11:26 GMT

←Older revision		Revision as of 01:11, 25 December 2014
Line 2:		Line 2:
	<StructureSection load='3fyd' size='340' side='right' caption='[[3fyd]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='3fyd' size='340' side='right' caption='[[3fyd]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fyd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FYD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fyd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FYD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA, MJ1029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=3fyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fyd RCSB], [http://www.ebi.ac.uk/pdbsum/3fyd 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=3fyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fyd RCSB], [http://www.ebi.ac.uk/pdbsum/3fyd PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RSMA_METJA RSMA_METJA]] Specifically dimethylates two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits.[HAMAP-Rule:MF_00607]<ref>PMID:19520088</ref> <ref>PMID:20163168</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 43067]]
	[[Category: Musayev, F N]]		[[Category: Musayev, F N]]
	[[Category: Rife, J P]]		[[Category: Rife, J P]]

OCA at 07:23, 12 November 2014

OCA — Wed, 12 Nov 2014 07:23:59 GMT

←Older revision		Revision as of 07:23, 12 November 2014
Line 2:		Line 2:
	<StructureSection load='3fyd' size='340' side='right' caption='[[3fyd]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='3fyd' size='340' side='right' caption='[[3fyd]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fyd]] is a 1 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FYD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fyd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FYD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA, MJ1029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</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=3fyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fyd RCSB], [http://www.ebi.ac.uk/pdbsum/3fyd 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=3fyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fyd RCSB], [http://www.ebi.ac.uk/pdbsum/3fyd PDBsum]</span></td></tr>
	</table>		</table>
Line 30:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	~~[[Category: Methanocaldococcus jannaschii]]~~	+	[[Category: Musayev, F N]]
-	[[Category: Musayev, F N.]]	+	[[Category: Rife, J P]]
-	[[Category: Rife, J P.]]	+	[[Category: Scarsdale, J N]]
-	[[Category: Scarsdale, J N.]]	+
	[[Category: Dimethyladenosine transferase]]		[[Category: Dimethyladenosine transferase]]
	[[Category: Methyltransferase]]		[[Category: Methyltransferase]]

OCA at 14:06, 3 November 2014

OCA — Mon, 03 Nov 2014 14:06:34 GMT

←Older revision		Revision as of 14:06, 3 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3fyd.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Dim1 from the thermophilic archeon, Methanocaldococcus jannaschi==
		+	<StructureSection load='3fyd' size='340' side='right' caption='[[3fyd]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3fyd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FYD FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA, MJ1029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</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=3fyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fyd RCSB], [http://www.ebi.ac.uk/pdbsum/3fyd 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/fy/3fyd_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 ==
		+	The enzymes of the KsgA/Dim1 family are universally distributed throughout all phylogeny; however, structural and functional differences are known to exist. The well-characterized function of these enzymes is to dimethylate two adjacent adenosines of the small ribosomal subunit in the normal course of ribosome maturation, and the structures of KsgA from Escherichia coli and Dim1 from Homo sapiens and Plasmodium falciparum have been determined. To this point, no examples of archaeal structures have been reported. Here, we report the structure of Dim1 from the thermophilic archaeon Methanocaldococcus jannaschii. While it shares obvious similarities with the bacterial and eukaryotic orthologs, notable structural differences exist among the three members, particularly in the C-terminal domain. Previous work showed that eukaryotic and archaeal Dim1 were able to robustly complement for KsgA in E. coli. Here, we repeated similar experiments to test for complementarity of archaeal Dim1 and bacterial KsgA in Saccharomyces cerevisiae. However, neither the bacterial nor the archaeal ortholog could complement for the eukaryotic Dim1. This might be related to the secondary, non-methyltransferase function that Dim1 is known to play in eukaryotic ribosomal maturation. To further delineate regions of the eukaryotic Dim1 critical to its function, we created and tested KsgA/Dim1 chimeras. Of the chimeras, only one constructed with the N-terminal domain from eukaryotic Dim1 and the C-terminal domain from archaeal Dim1 was able to complement, suggesting that eukaryotic-specific Dim1 function resides in the N-terminal domain also, where few structural differences are observed between members of the KsgA/Dim1 family. Future work is required to identify those determinants directly responsible for Dim1 function in ribosome biogenesis. Finally, we have conclusively established that none of the methyl groups are critically important to growth in yeast under standard conditions at a variety of temperatures.

-	~~{{STRUCTURE_3fyd\| PDB=3fyd \| SCENE= }}~~	+	Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases.,Pulicherla N, Pogorzala LA, Xu Z, O Farrell HC, Musayev FN, Scarsdale JN, Sia EA, Culver GM, Rife JP J Mol Biol. 2009 Sep 4;391(5):884-93. Epub 2009 Jun 9. PMID:19520088<ref>PMID:19520088</ref>

-	~~===Crystal Structure~~ of ~~Dim1 from~~ the ~~thermophilic archeon, Methanocaldococcus jannaschi===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19520088}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3fyd]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3FYD OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019520088<~~/~~ref~~><~~ref group="xtra">PMID:015136037</ref><references group="xtra"~~/>	+
	[[Category: Methanocaldococcus jannaschii]]		[[Category: Methanocaldococcus jannaschii]]
	[[Category: Musayev, F N.]]		[[Category: Musayev, F N.]]
Line 20:		Line 38:
	[[Category: Ribosomal assembly]]		[[Category: Ribosomal assembly]]
	[[Category: Rna-binding]]		[[Category: Rna-binding]]
-	[[Category: ~~Rossman~~ fold]]	+	[[Category: Rossmann fold]]
	[[Category: Rrna methylase]]		[[Category: Rrna methylase]]
	[[Category: Rrna processing]]		[[Category: Rrna processing]]
	[[Category: S-adenosyl-l-methionine]]		[[Category: S-adenosyl-l-methionine]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 14:30, 20 February 2013

OCA — Wed, 20 Feb 2013 14:30:32 GMT

←Older revision		Revision as of 14:30, 20 February 2013
Line 1:		Line 1:
	[[Image:3fyd.png\|left\|200px]]		[[Image:3fyd.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3fyd", 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_3fyd\| PDB=3fyd \| SCENE= }}		{{STRUCTURE_3fyd\| PDB=3fyd \| SCENE= }}

	===Crystal Structure of Dim1 from the thermophilic archeon, Methanocaldococcus jannaschi===		===Crystal Structure of Dim1 from the thermophilic archeon, Methanocaldococcus jannaschi===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19520088}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19520088 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19520088}}		{{ABSTRACT_PUBMED_19520088}}

Line 22:		Line 11:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19520088~~</ref><ref group="xtra">PMID:~~15136037~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019520088</ref><ref group="xtra">PMID:015136037</ref><references group="xtra"/>
	[[Category: Methanocaldococcus jannaschii]]		[[Category: Methanocaldococcus jannaschii]]
	[[Category: Musayev, F N.]]		[[Category: Musayev, F N.]]

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

OCA — Mon, 14 Mar 2011 19:52:52 GMT

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

←Older revision

Revision as of 19:52, 14 March 2011

OCA at 19:52, 14 March 2011

OCA — Mon, 14 Mar 2011 19:52:50 GMT

←Older revision		Revision as of 19:52, 14 March 2011
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-	{{Seed}}
	[[Image:3fyd.png\|left\|200px]]		[[Image:3fyd.png\|left\|200px]]

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	==About this Structure==		==About this Structure==
-	~~3FYD~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYD OCA].	+	[[3fyd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYD OCA].

	==Reference==		==Reference==
Line 37:		Line 36:
	[[Category: S-adenosyl-l-methionine]]		[[Category: S-adenosyl-l-methionine]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Sep 3 16:31:03 2009''