2ko6 - Revision history

OCA at 06:47, 1 May 2024

2024-05-01T06:47:15Z

←Older revision		Revision as of 06:47, 1 May 2024
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	==Solution structure of protein sf3929 from Shigella flexneri 2a. Northeast Structural Genomics Consortium target SfR81/Ontario Center for Structural Proteomics Target sf3929==		==Solution structure of protein sf3929 from Shigella flexneri 2a. Northeast Structural Genomics Consortium target SfR81/Ontario Center for Structural Proteomics Target sf3929==
-	<StructureSection load='2ko6' size='340' side='right'caption='[[2ko6~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='2ko6' size='340' side='right'caption='[[2ko6]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ko6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"shigella_paradysenteriae"_weldin_1927 "shigella paradysenteriae" weldin 1927~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KO6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KO6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ko6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Shigella_flexneri Shigella flexneri]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KO6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KO6 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>yihD, S3818, SF3929 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~623~~ "~~Shigella paradysenteriae~~" ~~Weldin 1927])~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2ko6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ko6 OCA], [https://pdbe.org/2ko6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ko6 RCSB], [https://www.ebi.ac.uk/pdbsum/2ko6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ko6 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=2ko6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ko6 OCA], [https://pdbe.org/2ko6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ko6 RCSB], [https://www.ebi.ac.uk/pdbsum/2ko6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ko6 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A384LJ77_SHIFL A0A384LJ77_SHIFL]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 17:		Line 19:
	</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=2ko6 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=2ko6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution - especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure determination, we developed a semi-automated strategy that utilizes non-uniform sampling (NUS) and multidimensional decomposition (MDD) for optimal data collection and processing of selected, high resolution multidimensional NMR experiments, combined it with an ABACUS protocol for sequential and side chain resonance assignments, and streamlined this procedure to execute structure and refinement calculations in CYANA and CNS, respectively. Two graphical user interfaces (GUIs) were developed to facilitate efficient analysis and compilation of the data and to guide automated structure determination. This integrated method was implemented and refined on over 30 high quality structures of proteins ranging from 5.5 to 16.5 kDa in size.
-
-	A novel strategy for NMR resonance assignment and protein structure determination.,Lemak A, Gutmanas A, Chitayat S, Karra M, Fares C, Sunnerhagen M, Arrowsmith CH J Biomol NMR. 2011 Jan;49(1):27-38. Epub 2010 Dec 14. PMID:21161328<ref>PMID:21161328</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2ko6" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Shigella paradysenteriae weldin 1927]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Arrowsmith, C H~~]]	+	[[Category: Shigella flexneri]]
-	[[Category: ~~Fares, C~~]]	+	[[Category: Arrowsmith CH]]
-	[[Category: ~~Lemak, A~~]]	+	[[Category: Fares C]]
-	[[Category: ~~Structural genomic]]~~	+	[[Category: Lemak A]]
-	~~[[Category: OCSP, Ontario Centre for Structural Proteomics~~]]	+	[[Category: Semest A]]
-	[[Category: Semest, A]]	+	[[Category: Wu B]]
-	[[Category: Wu, B]]	+	[[Category: Yee A]]
-	[[Category: Yee, A]]	+
-	~~[[Category: Alpha protein]]~~	+
-	~~[[Category: Nesg]]~~	+
-	~~[[Category: Ocsp]]~~	+
-	~~[[Category: Ontario centre for structural proteomic]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Unknown function~~]]	+

OCA at 07:08, 1 December 2021

2021-12-01T07:08:14Z

←Older revision		Revision as of 07:08, 1 December 2021
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	<StructureSection load='2ko6' size='340' side='right'caption='[[2ko6]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2ko6' size='340' side='right'caption='[[2ko6]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ko6]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"shigella_paradysenteriae"_weldin_1927 "shigella paradysenteriae" weldin 1927]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KO6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2KO6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ko6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"shigella_paradysenteriae"_weldin_1927 "shigella paradysenteriae" weldin 1927]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KO6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KO6 FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yihD, S3818, SF3929 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=623 "Shigella paradysenteriae" Weldin 1927])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yihD, S3818, SF3929 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=623 "Shigella paradysenteriae" Weldin 1927])</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=2ko6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ko6 OCA], [~~http~~://pdbe.org/2ko6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ko6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ko6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ko6 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=2ko6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ko6 OCA], [https://pdbe.org/2ko6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ko6 RCSB], [https://www.ebi.ac.uk/pdbsum/2ko6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ko6 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 09:41, 26 February 2020

2020-02-26T09:41:29Z

←Older revision		Revision as of 09:41, 26 February 2020
Line 1:		Line 1:

	==Solution structure of protein sf3929 from Shigella flexneri 2a. Northeast Structural Genomics Consortium target SfR81/Ontario Center for Structural Proteomics Target sf3929==		==Solution structure of protein sf3929 from Shigella flexneri 2a. Northeast Structural Genomics Consortium target SfR81/Ontario Center for Structural Proteomics Target sf3929==
-	<StructureSection load='2ko6' size='340' side='right' caption='[[2ko6]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='2ko6' size='340' side='right'caption='[[2ko6]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ko6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"shigella_paradysenteriae"_weldin_1927 "shigella paradysenteriae" weldin 1927]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KO6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KO6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ko6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"shigella_paradysenteriae"_weldin_1927 "shigella paradysenteriae" weldin 1927]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KO6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KO6 FirstGlance]. <br>
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Shigella paradysenteriae weldin 1927]]		[[Category: Shigella paradysenteriae weldin 1927]]
		+	[[Category: Large Structures]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
	[[Category: Fares, C]]		[[Category: Fares, C]]

OCA at 07:48, 25 July 2018

2018-07-25T07:48:34Z

←Older revision		Revision as of 07:48, 25 July 2018
Line 1:		Line 1:
		+
	==Solution structure of protein sf3929 from Shigella flexneri 2a. Northeast Structural Genomics Consortium target SfR81/Ontario Center for Structural Proteomics Target sf3929==		==Solution structure of protein sf3929 from Shigella flexneri 2a. Northeast Structural Genomics Consortium target SfR81/Ontario Center for Structural Proteomics Target sf3929==
	<StructureSection load='2ko6' size='340' side='right' caption='[[2ko6]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2ko6' size='340' side='right' caption='[[2ko6]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2ko6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"shigella_paradysenteriae"_weldin_1927 "shigella paradysenteriae" weldin 1927]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KO6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KO6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ko6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"shigella_paradysenteriae"_weldin_1927 "shigella paradysenteriae" weldin 1927]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KO6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KO6 FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yihD, S3818, SF3929 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=623 "Shigella paradysenteriae" Weldin 1927])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yihD, S3818, SF3929 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=623 "Shigella paradysenteriae" Weldin 1927])</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=2ko6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ko6 OCA], [http://pdbe.org/2ko6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ko6 RCSB], [http://www.ebi.ac.uk/pdbsum/2ko6 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=2ko6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ko6 OCA], [http://pdbe.org/2ko6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ko6 RCSB], [http://www.ebi.ac.uk/pdbsum/2ko6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ko6 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ko/2ko6_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ko/2ko6_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 14:20, 9 February 2016

2016-02-09T14:20:53Z

←Older revision		Revision as of 14:20, 9 February 2016
Line 14:		Line 14:
	<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=2ko6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:05, 10 September 2015

2015-09-10T23:05:02Z

←Older revision		Revision as of 23:05, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2ko6' size='340' side='right' caption='[[2ko6]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2ko6' size='340' side='right' caption='[[2ko6]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ko6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Shigella_flexneri Shigella flexneri~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KO6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KO6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ko6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"shigella_paradysenteriae"_weldin_1927 "shigella paradysenteriae" weldin 1927]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KO6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KO6 FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yihD, S3818, SF3929 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=623 Shigella ~~flexneri~~])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yihD, S3818, SF3929 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=623 "Shigella paradysenteriae" Weldin 1927])</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=2ko6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ko6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ko6 RCSB], [http://www.ebi.ac.uk/pdbsum/2ko6 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=2ko6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ko6 OCA], [http://pdbe.org/2ko6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ko6 RCSB], [http://www.ebi.ac.uk/pdbsum/2ko6 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 24:		Line 24:
	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 2ko6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Shigella ~~flexneri~~]]	+	[[Category: Shigella paradysenteriae weldin 1927]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
	[[Category: Fares, C]]		[[Category: Fares, C]]

OCA at 14:46, 19 January 2015

2015-01-19T14:46:25Z

←Older revision		Revision as of 14:46, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ko6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Shigella_flexneri Shigella flexneri]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KO6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KO6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ko6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Shigella_flexneri Shigella flexneri]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KO6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KO6 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yihD, S3818, SF3929 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=623 Shigella flexneri])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yihD, S3818, SF3929 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=623 Shigella flexneri])</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=2ko6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ko6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ko6 RCSB], [http://www.ebi.ac.uk/pdbsum/2ko6 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=2ko6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ko6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ko6 RCSB], [http://www.ebi.ac.uk/pdbsum/2ko6 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Shigella flexneri]]		[[Category: Shigella flexneri]]
-	[[Category: Arrowsmith, C H.]]	+	[[Category: Arrowsmith, C H]]
-	[[Category: Fares, C.]]	+	[[Category: Fares, C]]
-	[[Category: Lemak, A.]]	+	[[Category: Lemak, A]]
-	[[Category: ~~NESG, Northeast~~ Structural ~~Genomics Consortium.~~]]	+	[[Category: Structural genomic]]
-	[[Category: OCSP, Ontario Centre for Structural Proteomics.]]	+	[[Category: OCSP, Ontario Centre for Structural Proteomics]]
-	[[Category: Semest, A.]]	+	[[Category: Semest, A]]
-	[[Category: Wu, B.]]	+	[[Category: Wu, B]]
-	[[Category: Yee, A.]]	+	[[Category: Yee, A]]
	[[Category: Alpha protein]]		[[Category: Alpha protein]]
	[[Category: Nesg]]		[[Category: Nesg]]
-	[[Category: Northeast structural genomics consortium]]
	[[Category: Ocsp]]		[[Category: Ocsp]]
	[[Category: Ontario centre for structural proteomic]]		[[Category: Ontario centre for structural proteomic]]
-	[[Category: Protein structure initiative]]	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category: Psi-2]]~~	+
-	~~[[Category: Structural genomic~~]]	+
	[[Category: Unknown function]]		[[Category: Unknown function]]

OCA at 08:46, 3 October 2014

2014-10-03T08:46:17Z

←Older revision		Revision as of 08:46, 3 October 2014
Line 2:		Line 2:
	<StructureSection load='2ko6' size='340' side='right' caption='[[2ko6]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2ko6' size='340' side='right' caption='[[2ko6]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ko6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Shigella_flexneri Shigella flexneri]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KO6 OCA]. <br>	+	<table><tr><td colspan='2'>[[2ko6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Shigella_flexneri Shigella flexneri]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KO6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KO6 FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yihD, S3818, SF3929 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=623 Shigella flexneri])</td></tr>		</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yihD, S3818, SF3929 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=623 Shigella flexneri])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=2ko6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ko6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ko6 RCSB], [http://www.ebi.ac.uk/pdbsum/2ko6 PDBsum]</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=2ko6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ko6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ko6 RCSB], [http://www.ebi.ac.uk/pdbsum/2ko6 PDBsum]</span></td></tr>
	<table>		<table>
Line 23:		Line 22:
	A novel strategy for NMR resonance assignment and protein structure determination.,Lemak A, Gutmanas A, Chitayat S, Karra M, Fares C, Sunnerhagen M, Arrowsmith CH J Biomol NMR. 2011 Jan;49(1):27-38. Epub 2010 Dec 14. PMID:21161328<ref>PMID:21161328</ref>		A novel strategy for NMR resonance assignment and protein structure determination.,Lemak A, Gutmanas A, Chitayat S, Karra M, Fares C, Sunnerhagen M, Arrowsmith CH J Biomol NMR. 2011 Jan;49(1):27-38. Epub 2010 Dec 14. PMID:21161328<ref>PMID:21161328</ref>

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

OCA at 09:38, 1 May 2014

2014-05-01T09:38:24Z

←Older revision		Revision as of 09:38, 1 May 2014
Line 2:		Line 2:
	<StructureSection load='2ko6' size='340' side='right' caption='[[2ko6]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2ko6' size='340' side='right' caption='[[2ko6]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	[[2ko6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Shigella_flexneri Shigella flexneri]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KO6 OCA]. <br>	+	<table><tr><td colspan='2'>[[2ko6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Shigella_flexneri Shigella flexneri]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KO6 OCA]. <br>
-	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>	+	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yihD, S3818, SF3929 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=623 Shigella flexneri])</td></tr>
-	<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ko6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ko6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ko6 RCSB], [http://www.ebi.ac.uk/pdbsum/2ko6 PDBsum]</span><br>	+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=2ko6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ko6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ko6 RCSB], [http://www.ebi.ac.uk/pdbsum/2ko6 PDBsum]</span></td></tr>
		+	<table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
-	[[Image:Consurf_key_small.gif\|right]]	+	[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
Line 15:		Line 17:
	</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/chain_selection.php?pdb_ID=2ata ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution - especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure determination, we developed a semi-automated strategy that utilizes non-uniform sampling (NUS) and multidimensional decomposition (MDD) for optimal data collection and processing of selected, high resolution multidimensional NMR experiments, combined it with an ABACUS protocol for sequential and side chain resonance assignments, and streamlined this procedure to execute structure and refinement calculations in CYANA and CNS, respectively. Two graphical user interfaces (GUIs) were developed to facilitate efficient analysis and compilation of the data and to guide automated structure determination. This integrated method was implemented and refined on over 30 high quality structures of proteins ranging from 5.5 to 16.5 kDa in size.		The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution - especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure determination, we developed a semi-automated strategy that utilizes non-uniform sampling (NUS) and multidimensional decomposition (MDD) for optimal data collection and processing of selected, high resolution multidimensional NMR experiments, combined it with an ABACUS protocol for sequential and side chain resonance assignments, and streamlined this procedure to execute structure and refinement calculations in CYANA and CNS, respectively. Two graphical user interfaces (GUIs) were developed to facilitate efficient analysis and compilation of the data and to guide automated structure determination. This integrated method was implemented and refined on over 30 high quality structures of proteins ranging from 5.5 to 16.5 kDa in size.
Line 21:		Line 24:

	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>		From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:58, 30 April 2014

2014-04-30T09:58:21Z

←Older revision		Revision as of 09:58, 30 April 2014
Line 4:		Line 4:
	[[2ko6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Shigella_flexneri Shigella flexneri]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KO6 OCA]. <br>		[[2ko6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Shigella_flexneri Shigella flexneri]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KO6 OCA]. <br>
	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>		<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
		+	<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ko6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ko6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ko6 RCSB], [http://www.ebi.ac.uk/pdbsum/2ko6 PDBsum]</span><br>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|right]]		[[Image:Consurf_key_small.gif\|right]]