2rhl - Revision history

OCA at 09:22, 21 February 2024

OCA — Wed, 21 Feb 2024 09:22:23 GMT

←Older revision		Revision as of 09:22, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='2rhl' size='340' side='right'caption='[[2rhl]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='2rhl' size='340' side='right'caption='[[2rhl]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rhl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RHL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rhl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RHL FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GDP:GUANOSINE~~-~~5-DIPHOSPHATE'>GDP</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.45Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2rhh\|2rhh]], [[2rhj\|2rhj]], [[2rho\|2rho]]~~</~~div~~>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ftsZ ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=2rhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhl OCA], [https://pdbe.org/2rhl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rhl RCSB], [https://www.ebi.ac.uk/pdbsum/2rhl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rhl 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=2rhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhl OCA], [https://pdbe.org/2rhl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rhl RCSB], [https://www.ebi.ac.uk/pdbsum/2rhl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rhl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/FTSZ_BACSU FTSZ_BACSU]] Essential cell division protein that forms a contractile ring structure (Z ring) at the future cell division site. The regulation of the ring assembly controls the timing and the location of cell division. One of the functions of the FtsZ ring is to recruit other cell division proteins to the septum to produce a new cell wall between the dividing cells. Binds GTP and shows GTPase activity.<ref>PMID:15317782</ref> <ref>PMID:16159787</ref>	+	[https://www.uniprot.org/uniprot/FTSZ_BACSU FTSZ_BACSU] Essential cell division protein that forms a contractile ring structure (Z ring) at the future cell division site. The regulation of the ring assembly controls the timing and the location of cell division. One of the functions of the FtsZ ring is to recruit other cell division proteins to the septum to produce a new cell wall between the dividing cells. Binds GTP and shows GTPase activity.<ref>PMID:15317782</ref> <ref>PMID:16159787</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=2rhl 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=2rhl ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	BACKGROUND: With the goal of improving yield and success rates of heterologous protein production for structural studies we have developed the database and algorithm software package Gene Composer. This freely available electronic tool facilitates the information-rich design of protein constructs and their engineered synthetic gene sequences, as detailed in the accompanying manuscript. RESULTS: In this report, we compare heterologous protein expression levels from native sequences to that of codon engineered synthetic gene constructs designed by Gene Composer. A test set of proteins including a human kinase (P38alpha), viral polymerase (HCV NS5B), and bacterial structural protein (FtsZ) were expressed in both E. coli and a cell-free wheat germ translation system. We also compare the protein expression levels in E. coli for a set of 11 different proteins with greatly varied G:C content and codon bias. CONCLUSION: The results consistently demonstrate that protein yields from codon engineered Gene Composer designs are as good as or better than those achieved from the synonymous native genes. Moreover, structure guided N- and C-terminal deletion constructs designed with the aid of Gene Composer can lead to greater success in gene to structure work as exemplified by the X-ray crystallographic structure determination of FtsZ from Bacillus subtilis. These results validate the Gene Composer algorithms, and suggest that using a combination of synthetic gene and protein construct engineering tools can improve the economics of gene to structure research.
-
-	Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using Gene Composer.,Raymond A, Lovell S, Lorimer D, Walchli J, Mixon M, Wallace E, Thompkins K, Archer K, Burgin A, Stewart L BMC Biotechnol. 2009 Apr 21;9:37. PMID:19383143<ref>PMID:19383143</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2rhl" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~globigii migula 1900~~]]	+	[[Category: Bacillus subtilis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: ATCG3D, Accelerated Technologies Center for Gene to 3D Structure]]~~	+	[[Category: Burgin A]]
-	[[Category: Burgin, A]]	+	[[Category: Halloran Z]]
-	[[Category: Halloran, Z]]	+	[[Category: Hjerrild K]]
-	[[Category: Hjerrild, K]]	+	[[Category: Lovell S]]
-	[[Category: Lovell, S]]	+	[[Category: Sheridan D]]
-	[[Category: Sheridan, D]]	+	[[Category: Stewart L]]
-	[[Category: Stewart, L]]	+
-	~~[[Category: Accelerated technologies center for gene to 3d structure]]~~	+
-	~~[[Category: Atcg3d]]~~	+
-	~~[[Category: Cell cycle]]~~	+
-	~~[[Category: Cell division protein]]~~	+
-	~~[[Category: Gtp-binding]]~~	+
-	~~[[Category: Gtpase]]~~	+
-	~~[[Category: Polymerization]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Tubulin homolog~~]]	+

OCA at 04:25, 2 July 2021

OCA — Fri, 02 Jul 2021 04:25:41 GMT

←Older revision		Revision as of 04:25, 2 July 2021
Line 1:		Line 1:

	==Synthetic Gene Encoded Bacillus Subtilis FtsZ NCS Dimer with Bound GDP==		==Synthetic Gene Encoded Bacillus Subtilis FtsZ NCS Dimer with Bound GDP==
-	<StructureSection load='2rhl' size='340' side='right' caption='[[2rhl]], [[Resolution\|resolution]] 2.45Å' scene=''>	+	<StructureSection load='2rhl' size='340' side='right'caption='[[2rhl]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rhl]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2RHL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rhl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RHL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rhh\|2rhh]], [[2rhj\|2rhj]], [[2rho\|2rho]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2rhh\|2rhh]], [[2rhj\|2rhj]], [[2rho\|2rho]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ftsZ ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ftsZ ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=2rhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhl OCA], [~~http~~://pdbe.org/2rhl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2rhl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2rhl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2rhl 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=2rhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhl OCA], [https://pdbe.org/2rhl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rhl RCSB], [https://www.ebi.ac.uk/pdbsum/2rhl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rhl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/FTSZ_BACSU FTSZ_BACSU]] Essential cell division protein that forms a contractile ring structure (Z ring) at the future cell division site. The regulation of the ring assembly controls the timing and the location of cell division. One of the functions of the FtsZ ring is to recruit other cell division proteins to the septum to produce a new cell wall between the dividing cells. Binds GTP and shows GTPase activity.<ref>PMID:15317782</ref> <ref>PMID:16159787</ref>	+	[[https://www.uniprot.org/uniprot/FTSZ_BACSU FTSZ_BACSU]] Essential cell division protein that forms a contractile ring structure (Z ring) at the future cell division site. The regulation of the ring assembly controls the timing and the location of cell division. One of the functions of the FtsZ ring is to recruit other cell division proteins to the septum to produce a new cell wall between the dividing cells. Binds GTP and shows GTPase activity.<ref>PMID:15317782</ref> <ref>PMID:16159787</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rh/2rhl_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rh/2rhl_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>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 2rhl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2rhl" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cell division protein 3D structures\|Cell division protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus globigii migula 1900]]		[[Category: Bacillus globigii migula 1900]]
		+	[[Category: Large Structures]]
	[[Category: ATCG3D, Accelerated Technologies Center for Gene to 3D Structure]]		[[Category: ATCG3D, Accelerated Technologies Center for Gene to 3D Structure]]
	[[Category: Burgin, A]]		[[Category: Burgin, A]]

OCA at 07:52, 25 October 2017

OCA — Wed, 25 Oct 2017 07:52:00 GMT

←Older revision		Revision as of 07:52, 25 October 2017
Line 1:		Line 1:
		+
	==Synthetic Gene Encoded Bacillus Subtilis FtsZ NCS Dimer with Bound GDP==		==Synthetic Gene Encoded Bacillus Subtilis FtsZ NCS Dimer with Bound GDP==
	<StructureSection load='2rhl' size='340' side='right' caption='[[2rhl]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='2rhl' size='340' side='right' caption='[[2rhl]], [[Resolution\|resolution]] 2.45Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rhh\|2rhh]], [[2rhj\|2rhj]], [[2rho\|2rho]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rhh\|2rhh]], [[2rhj\|2rhj]], [[2rho\|2rho]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ftsZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ftsZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=2rhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhl OCA], [http://pdbe.org/2rhl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rhl RCSB], [http://www.ebi.ac.uk/pdbsum/2rhl 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=2rhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhl OCA], [http://pdbe.org/2rhl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rhl RCSB], [http://www.ebi.ac.uk/pdbsum/2rhl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rhl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 2rhl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2rhl" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Cell division protein Ftsz\|Cell division protein Ftsz]]
-	*[[Tubulin\|Tubulin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:07, 9 February 2016

OCA — Tue, 09 Feb 2016 13:07:53 GMT

←Older revision		Revision as of 13:07, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='2rhl' size='340' side='right' caption='[[2rhl]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='2rhl' size='340' side='right' caption='[[2rhl]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rhl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_subtilis Bacillus subtilis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RHL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rhl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RHL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rhh\|2rhh]], [[2rhj\|2rhj]], [[2rho\|2rho]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rhh\|2rhh]], [[2rhj\|2rhj]], [[2rho\|2rho]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ftsZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus ~~subtilis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ftsZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=2rhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rhl RCSB], [http://www.ebi.ac.uk/pdbsum/2rhl 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=2rhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhl OCA], [http://pdbe.org/2rhl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rhl RCSB], [http://www.ebi.ac.uk/pdbsum/2rhl PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	<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=2rhl ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 2rhl" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
		+	*[[Cell division protein Ftsz\|Cell division protein Ftsz]]
	*[[Tubulin\|Tubulin]]		*[[Tubulin\|Tubulin]]
	== References ==		== References ==
Line 35:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~subtilis~~]]	+	[[Category: Bacillus globigii migula 1900]]
	[[Category: ATCG3D, Accelerated Technologies Center for Gene to 3D Structure]]		[[Category: ATCG3D, Accelerated Technologies Center for Gene to 3D Structure]]
	[[Category: Burgin, A]]		[[Category: Burgin, A]]

OCA at 07:00, 25 December 2014

OCA — Thu, 25 Dec 2014 07:00:47 GMT

←Older revision		Revision as of 07:00, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rhl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RHL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rhl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RHL FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rhh\|2rhh]], [[2rhj\|2rhj]], [[2rho\|2rho]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rhh\|2rhh]], [[2rhj\|2rhj]], [[2rho\|2rho]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ftsZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ftsZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=2rhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rhl RCSB], [http://www.ebi.ac.uk/pdbsum/2rhl 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=2rhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rhl RCSB], [http://www.ebi.ac.uk/pdbsum/2rhl PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FTSZ_BACSU FTSZ_BACSU]] Essential cell division protein that forms a contractile ring structure (Z ring) at the future cell division site. The regulation of the ring assembly controls the timing and the location of cell division. One of the functions of the FtsZ ring is to recruit other cell division proteins to the septum to produce a new cell wall between the dividing cells. Binds GTP and shows GTPase activity.<ref>PMID:15317782</ref> <ref>PMID:16159787</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 30:

	==See Also==		==See Also==
-	*[[Cell division protein Ftsz\|Cell division protein Ftsz]]
	*[[Tubulin\|Tubulin]]		*[[Tubulin\|Tubulin]]
	== References ==		== References ==
Line 35:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
-	[[Category: ATCG3D, Accelerated Technologies Center for Gene to 3D Structure.]]	+	[[Category: ATCG3D, Accelerated Technologies Center for Gene to 3D Structure]]
-	[[Category: Burgin, A.]]	+	[[Category: Burgin, A]]
-	[[Category: Halloran, Z.]]	+	[[Category: Halloran, Z]]
-	[[Category: Hjerrild, K.]]	+	[[Category: Hjerrild, K]]
-	[[Category: Lovell, S.]]	+	[[Category: Lovell, S]]
-	[[Category: Sheridan, D.]]	+	[[Category: Sheridan, D]]
-	[[Category: Stewart, L.]]	+	[[Category: Stewart, L]]
	[[Category: Accelerated technologies center for gene to 3d structure]]		[[Category: Accelerated technologies center for gene to 3d structure]]
	[[Category: Atcg3d]]		[[Category: Atcg3d]]
Line 49:		Line 50:
	[[Category: Gtpase]]		[[Category: Gtpase]]
	[[Category: Polymerization]]		[[Category: Polymerization]]
-	[[Category: Protein structure initiative]]	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category: Psi-2~~]]	+
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Tubulin homolog]]		[[Category: Tubulin homolog]]

OCA at 06:37, 29 September 2014

OCA — Mon, 29 Sep 2014 06:37:41 GMT

←Older revision		Revision as of 06:37, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2rhl.~~png~~\|~~left~~\|200px]]	+	==Synthetic Gene Encoded Bacillus Subtilis FtsZ NCS Dimer with Bound GDP==
		+	<StructureSection load='2rhl' size='340' side='right' caption='[[2rhl]], [[Resolution\|resolution]] 2.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2rhl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RHL FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rhh\|2rhh]], [[2rhj\|2rhj]], [[2rho\|2rho]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ftsZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=2rhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rhl RCSB], [http://www.ebi.ac.uk/pdbsum/2rhl 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/rh/2rhl_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 ==
		+	BACKGROUND: With the goal of improving yield and success rates of heterologous protein production for structural studies we have developed the database and algorithm software package Gene Composer. This freely available electronic tool facilitates the information-rich design of protein constructs and their engineered synthetic gene sequences, as detailed in the accompanying manuscript. RESULTS: In this report, we compare heterologous protein expression levels from native sequences to that of codon engineered synthetic gene constructs designed by Gene Composer. A test set of proteins including a human kinase (P38alpha), viral polymerase (HCV NS5B), and bacterial structural protein (FtsZ) were expressed in both E. coli and a cell-free wheat germ translation system. We also compare the protein expression levels in E. coli for a set of 11 different proteins with greatly varied G:C content and codon bias. CONCLUSION: The results consistently demonstrate that protein yields from codon engineered Gene Composer designs are as good as or better than those achieved from the synonymous native genes. Moreover, structure guided N- and C-terminal deletion constructs designed with the aid of Gene Composer can lead to greater success in gene to structure work as exemplified by the X-ray crystallographic structure determination of FtsZ from Bacillus subtilis. These results validate the Gene Composer algorithms, and suggest that using a combination of synthetic gene and protein construct engineering tools can improve the economics of gene to structure research.

-	~~{{STRUCTURE_2rhl\| PDB=2rhl \| SCENE= }}~~	+	Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using Gene Composer.,Raymond A, Lovell S, Lorimer D, Walchli J, Mixon M, Wallace E, Thompkins K, Archer K, Burgin A, Stewart L BMC Biotechnol. 2009 Apr 21;9:37. PMID:19383143<ref>PMID:19383143</ref>

-	~~===Synthetic Gene Encoded Bacillus Subtilis FtsZ NCS Dimer with Bound GDP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19383143}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2rhl]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_subtilis Bacillus subtilis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2RHL OCA].~~	+

	==See Also==		==See Also==
	*[[Cell division protein Ftsz\|Cell division protein Ftsz]]		*[[Cell division protein Ftsz\|Cell division protein Ftsz]]
	*[[Tubulin\|Tubulin]]		*[[Tubulin\|Tubulin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019383143<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: ATCG3D, Accelerated Technologies Center for Gene to 3D Structure.]]		[[Category: ATCG3D, Accelerated Technologies Center for Gene to 3D Structure.]]

OCA at 13:56, 20 October 2012

OCA — Sat, 20 Oct 2012 13:56:57 GMT

←Older revision		Revision as of 13:56, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2rhl]] is a 2 chain structure ~~of [[Cell division protein Ftsz]] and [[Tubulin]]~~ with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHL OCA].	+	[[2rhl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHL OCA].

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

OCA at 13:35, 26 July 2012

OCA — Thu, 26 Jul 2012 13:35:58 GMT

←Older revision		Revision as of 13:35, 26 July 2012
Line 1:		Line 1:
	[[Image:2rhl.png\|left\|200px]]		[[Image:2rhl.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2rhl", 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_2rhl\| PDB=2rhl \| SCENE= }}		{{STRUCTURE_2rhl\| PDB=2rhl \| SCENE= }}

	===Synthetic Gene Encoded Bacillus Subtilis FtsZ NCS Dimer with Bound GDP===		===Synthetic Gene Encoded Bacillus Subtilis FtsZ NCS Dimer with Bound GDP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19383143}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19383143 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19383143}}		{{ABSTRACT_PUBMED_19383143}}

	==About this Structure==		==About this Structure==
-	[[2rhl]] is a 2 chain structure of [[Tubulin]] with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHL OCA].	+	[[2rhl]] is a 2 chain structure of [[Cell division protein Ftsz]] and [[Tubulin]] with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHL OCA].

	==See Also==		==See Also==
-	*[[Tubulin]]	+	*[[Cell division protein Ftsz\|Cell division protein Ftsz]]
		+	*[[Tubulin\|Tubulin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19383143~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019383143</ref><references group="xtra"/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: ATCG3D, Accelerated Technologies Center for Gene to 3D Structure.]]		[[Category: ATCG3D, Accelerated Technologies Center for Gene to 3D Structure.]]

OCA: Protected "2rhl" [edit=sysop:move=sysop]

OCA — Sun, 26 Dec 2010 08:41:17 GMT

Protected "2rhl" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:41, 26 December 2010

OCA at 08:41, 26 December 2010

OCA — Sun, 26 Dec 2010 08:41:16 GMT

←Older revision		Revision as of 08:41, 26 December 2010
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2rhl.png\|left\|200px]]		[[Image:2rhl.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~2RHL~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHL OCA].	+	[[2rhl]] is a 2 chain structure of [[Tubulin]] with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHL OCA].
		+
		+	==See Also==
		+	*[[Tubulin]]

	==Reference==		==Reference==
Line 43:		Line 45:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Tubulin homolog]]		[[Category: Tubulin homolog]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Sep 3 16:26:09 2009''