1via - Revision history

OCA at 00:04, 28 December 2023

OCA — Thu, 28 Dec 2023 00:04:12 GMT

←Older revision		Revision as of 00:04, 28 December 2023
Line 3:		Line 3:
	<StructureSection load='1via' size='340' side='right'caption='[[1via]], [[Resolution\|resolution]] 1.57Å' scene=''>		<StructureSection load='1via' size='340' side='right'caption='[[1via]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1via]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"campylobacter_fetus_subsp._jejuni"_smibert_1974 "campylobacter fetus subsp.~~ jejuni~~" smibert 1974~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1VIA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1via]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Campylobacter_jejuni Campylobacter jejuni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VIA 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]] 1.57Å</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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">aroK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197 "Campylobacter fetus subsp. jejuni" Smibert 1974])</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=1via FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1via OCA], [https://pdbe.org/1via PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1via RCSB], [https://www.ebi.ac.uk/pdbsum/1via PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1via ProSAT]</span></td></tr>
-	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:~~</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Shikimate_kinase Shikimate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.71 2.7.1.71] </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=1via FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1via OCA], [~~http~~://pdbe.org/1via PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1via RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1via PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1via ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q0PBC3_CAMJE Q0PBC3_CAMJE] Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate.[HAMAP-Rule:MF_00109]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Shikimate kinase\|Shikimate kinase]]	+	*[[Shikimate kinase 3D structures\|Shikimate kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Campylobacter ~~fetus subsp.~~ jejuni ~~smibert 1974~~]]	+	[[Category: Campylobacter jejuni]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Shikimate kinase]]~~	+	[[Category: Structural GenomiX]]
-	~~[[Category:~~ GenomiX~~, Structural]]~~	+
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:37, 30 December 2020

OCA — Wed, 30 Dec 2020 07:37:23 GMT

OCA at 07:50, 4 April 2018

OCA — Wed, 04 Apr 2018 07:50:19 GMT

←Older revision		Revision as of 07:50, 4 April 2018
Line 1:		Line 1:
		+
	==Crystal structure of shikimate kinase==		==Crystal structure of shikimate kinase==
	<StructureSection load='1via' size='340' side='right' caption='[[1via]], [[Resolution\|resolution]] 1.57Å' scene=''>		<StructureSection load='1via' size='340' side='right' caption='[[1via]], [[Resolution\|resolution]] 1.57Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aroK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197 "Campylobacter fetus subsp. jejuni" Smibert 1974])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aroK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197 "Campylobacter fetus subsp. jejuni" Smibert 1974])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Shikimate_kinase Shikimate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.71 2.7.1.71] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Shikimate_kinase Shikimate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.71 2.7.1.71] </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=1via FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1via OCA], [http://pdbe.org/1via PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1via RCSB], [http://www.ebi.ac.uk/pdbsum/1via 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=1via FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1via OCA], [http://pdbe.org/1via PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1via RCSB], [http://www.ebi.ac.uk/pdbsum/1via PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1via ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vi/1via_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vi/1via_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>
	</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=1via ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:39, 11 September 2015

OCA — Fri, 11 Sep 2015 15:39:16 GMT

←Older revision		Revision as of 15:39, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1via' size='340' side='right' caption='[[1via]], [[Resolution\|resolution]] 1.57Å' scene=''>		<StructureSection load='1via' size='340' side='right' caption='[[1via]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1via]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Campylobacter_jejuni Campylobacter~~ jejuni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VIA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1via]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"campylobacter_fetus_subsp._jejuni"_smibert_1974 "campylobacter fetus subsp. jejuni" smibert 1974]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VIA 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='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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aroK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197 Campylobacter jejuni])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aroK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197 "Campylobacter fetus subsp. jejuni" Smibert 1974])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Shikimate_kinase Shikimate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.71 2.7.1.71] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Shikimate_kinase Shikimate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.71 2.7.1.71] </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=1via FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1via OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1via RCSB], [http://www.ebi.ac.uk/pdbsum/1via 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=1via FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1via OCA], [http://pdbe.org/1via PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1via RCSB], [http://www.ebi.ac.uk/pdbsum/1via PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	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 1via" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Campylobacter jejuni]]	+	[[Category: Campylobacter fetus subsp. jejuni smibert 1974]]
	[[Category: Shikimate kinase]]		[[Category: Shikimate kinase]]
	[[Category: GenomiX, Structural]]		[[Category: GenomiX, Structural]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 13:11, 6 January 2015

OCA — Tue, 06 Jan 2015 13:11:20 GMT

OCA at 21:39, 29 September 2014

OCA — Mon, 29 Sep 2014 21:39:55 GMT

←Older revision		Revision as of 21:39, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1via.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of shikimate kinase==
		+	<StructureSection load='1via' size='340' side='right' caption='[[1via]], [[Resolution\|resolution]] 1.57Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1via]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_jejuni Campylobacter jejuni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VIA FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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>[[Gene\|Gene:]]</b></td><td class="sblockDat">aroK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197 Campylobacter jejuni])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Shikimate_kinase Shikimate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.71 2.7.1.71] </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=1via FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1via OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1via RCSB], [http://www.ebi.ac.uk/pdbsum/1via 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/vi/1via_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 targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB.

-	~~{{STRUCTURE_1via\| PDB=1via \| SCENE= }}~~	+	Structural analysis of a set of proteins resulting from a bacterial genomics project.,Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG, Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S, Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA, Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW, Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A, Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J, Winhoven J, Wright TA, Wu L, Xu J, Harris TJ Proteins. 2005 Sep 1;60(4):787-96. PMID:16021622<ref>PMID:16021622</ref>

-	~~===Crystal structure~~ of ~~shikimate kinase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_16021622}}~~	+	==See Also==
-		+	*[[Shikimate kinase\|Shikimate kinase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1via~~]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_jejuni Campylobacter jejuni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIA OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:016021622<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Campylobacter jejuni]]		[[Category: Campylobacter jejuni]]
	[[Category: Shikimate kinase]]		[[Category: Shikimate kinase]]

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

OCA — Sat, 05 Jan 2013 13:03:36 GMT

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

←Older revision

Revision as of 13:03, 5 January 2013

OCA at 13:03, 5 January 2013

OCA — Sat, 05 Jan 2013 13:03:32 GMT

←Older revision		Revision as of 13:03, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1via.png\|left\|200px]]		[[Image:1via.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1via", 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_1via\| PDB=1via \| SCENE= }}		{{STRUCTURE_1via\| PDB=1via \| SCENE= }}

	===Crystal structure of shikimate kinase===		===Crystal structure of shikimate kinase===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16021622}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16021622 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_16021622}}		{{ABSTRACT_PUBMED_16021622}}

	==About this Structure==		==About this Structure==
-	~~1VIA~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Campylobacter_jejuni Campylobacter jejuni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIA OCA].	+	[[1via]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_jejuni Campylobacter jejuni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIA OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16021622~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016021622</ref><references group="xtra"/>
	[[Category: Campylobacter jejuni]]		[[Category: Campylobacter jejuni]]
	[[Category: Shikimate kinase]]		[[Category: Shikimate kinase]]
	[[Category: GenomiX, Structural.]]		[[Category: GenomiX, Structural.]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Wed Feb 18 02:31:40 2009''~~	+

OCA at 00:31, 18 February 2009

OCA — Wed, 18 Feb 2009 00:31:41 GMT

←Older revision		Revision as of 00:31, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1VIA is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Campylobacter_jejuni Campylobacter jejuni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIA OCA].	+	1VIA is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Campylobacter_jejuni Campylobacter jejuni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIA OCA].

	==Reference==		==Reference==
-	Structural analysis of a set of proteins resulting from a bacterial genomics project., Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG, Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S, Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA, Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW, Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A, Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J, Winhoven J, Wright TA, Wu L, Xu J, Harris TJ, Proteins. 2005 Sep 1;60(4):787-96. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16021622 16021622]~~	+	<ref group="xtra">PMID:16021622</ref><references group="xtra"/>
	[[Category: Campylobacter jejuni]]		[[Category: Campylobacter jejuni]]
	[[Category: Shikimate kinase]]		[[Category: Shikimate kinase]]
-	[[Category: Single protein]]
	[[Category: GenomiX, Structural.]]		[[Category: GenomiX, Structural.]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 09~~:09:~~01 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 02:31:40 2009''

OCA at 06:09, 29 July 2008

OCA — Tue, 29 Jul 2008 06:09:05 GMT

←Older revision		Revision as of 06:09, 29 July 2008
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-	[[Image:1via.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1via.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_1via\| PDB=1via \| SCENE= }}		{{STRUCTURE_1via\| PDB=1via \| SCENE= }}

-	~~'''~~Crystal structure of shikimate kinase~~'''~~	+	===Crystal structure of shikimate kinase===


-	~~==Overview==~~	+	<!--
-	The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this ~~work was 80 structures~~, ~~covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of~~ the ~~remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed~~ to ~~deposit these structures in~~ the ~~Protein Data Bank, along with the associated X-ray diffraction data~~ (~~including refined experimental phases) and experimentally confirmed sequences~~. ~~BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3~~.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the ~~structural coverage of gene space is proceeding rapidly~~. ~~More distant sequence~~-~~structure relationships between the SGX and PDB structures were investigated using PDB~~-~~BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_16021622}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 16021622 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_16021622}}

	==About this Structure==		==About this Structure==
Line 25:		Line 29:
	[[Category: GenomiX, Structural.]]		[[Category: GenomiX, Structural.]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 12~~:33:44 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 09:09:01 2008''

←Older revision		Revision as of 07:37, 30 December 2020
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	==Crystal structure of shikimate kinase==		==Crystal structure of shikimate kinase==
-	<StructureSection load='1via' size='340' side='right' caption='[[1via]], [[Resolution\|resolution]] 1.57Å' scene=''>	+	<StructureSection load='1via' size='340' side='right'caption='[[1via]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1via]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"campylobacter_fetus_subsp._jejuni"_smibert_1974 "campylobacter fetus subsp. jejuni" smibert 1974]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIA OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1VIA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1via]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"campylobacter_fetus_subsp._jejuni"_smibert_1974 "campylobacter fetus subsp. jejuni" smibert 1974]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1VIA 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='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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aroK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197 "Campylobacter fetus subsp. jejuni" Smibert 1974])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aroK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197 "Campylobacter fetus subsp. jejuni" Smibert 1974])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Shikimate_kinase Shikimate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.71 2.7.1.71] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Shikimate_kinase Shikimate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.71 2.7.1.71] </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=1via FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1via OCA], [http://pdbe.org/1via PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1via RCSB], [http://www.ebi.ac.uk/pdbsum/1via PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1via 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=1via FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1via OCA], [http://pdbe.org/1via PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1via RCSB], [http://www.ebi.ac.uk/pdbsum/1via PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1via ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Campylobacter fetus subsp. jejuni smibert 1974]]		[[Category: Campylobacter fetus subsp. jejuni smibert 1974]]
		+	[[Category: Large Structures]]
	[[Category: Shikimate kinase]]		[[Category: Shikimate kinase]]
	[[Category: GenomiX, Structural]]		[[Category: GenomiX, Structural]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Transferase]]		[[Category: Transferase]]

←Older revision		Revision as of 13:11, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1via]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_jejuni Campylobacter jejuni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VIA FirstGlance]. <br>		<table><tr><td colspan='2'>[[1via]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_jejuni Campylobacter jejuni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VIA FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><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><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>[[Gene\|Gene:]]</b></td><td class="sblockDat">aroK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197 Campylobacter jejuni])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aroK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197 Campylobacter jejuni])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Shikimate_kinase Shikimate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.71 2.7.1.71] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Shikimate_kinase Shikimate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.71 2.7.1.71] </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=1via FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1via OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1via RCSB], [http://www.ebi.ac.uk/pdbsum/1via 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=1via FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1via OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1via RCSB], [http://www.ebi.ac.uk/pdbsum/1via PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: Campylobacter jejuni]]		[[Category: Campylobacter jejuni]]
	[[Category: Shikimate kinase]]		[[Category: Shikimate kinase]]
-	[[Category: GenomiX, Structural.]]	+	[[Category: GenomiX, Structural]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Transferase]]		[[Category: Transferase]]