1sdj - Revision history

OCA at 12:13, 6 March 2024

OCA — Wed, 06 Mar 2024 12:13:30 GMT

←Older revision		Revision as of 12:13, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='1sdj' size='340' side='right'caption='[[1sdj]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1sdj' size='340' side='right'caption='[[1sdj]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1sdj]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1p9v 1p9v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SDJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1SDJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1sdj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1p9v 1p9v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SDJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SDJ 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]] 2.3Å</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~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[1p9v\|1p9v]]~~</~~div~~>~~</td></tr>~~	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1sdj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sdj OCA], [https://pdbe.org/1sdj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sdj RCSB], [https://www.ebi.ac.uk/pdbsum/1sdj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sdj ProSAT], [https://www.topsan.org/Proteins/NESGC/1sdj TOPSAN]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YDDE, B1464 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1sdj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sdj OCA], [~~http~~://pdbe.org/1sdj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1sdj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1sdj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1sdj ProSAT], [~~http~~://www.topsan.org/Proteins/NESGC/1sdj TOPSAN]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/YDDE_ECOLI YDDE_ECOLI]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1sdj 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=1sdj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Phenazines produced by Pseudomonas and Streptomyces spp. are heterocyclic nitrogen-containing metabolites with antibiotic, antitumor, and antiparasitic activity. The antibiotic properties of pyocyanin, produced by Pseudomonas aeruginosa, were recognized in the 1890s, although this blue phenazine is now known to be a virulence factor in human disease. Despite their biological significance, the biosynthesis of phenazines is not fully understood. Here we present structural and functional studies of PhzF, an enzyme essential for phenazine synthesis in Pseudomonas spp. PhzF shares topology with diaminopimelate epimerase DapF but lacks the same catalytic residues. The structure of PhzF in complex with its substrate, trans-2,3-dihydro-3-hydroxyanthranilic acid, suggests that it is an isomerase using the conserved glutamate E45 to abstract a proton from C3 of the substrate. The proton is returned to C1 of the substrate after rearrangement of the double-bond system, yielding an enol that converts to the corresponding ketone. PhzF is a dimer that may be bifunctional, providing a shielded cavity for ketone dimerization via double Schiff-base formation to produce the phenazine scaffold. Our proposed mechanism is supported by mass and NMR spectroscopy. The results are discussed in the context of related structures and protein sequences of unknown biochemical function.
-
-	Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens.,Blankenfeldt W, Kuzin AP, Skarina T, Korniyenko Y, Tong L, Bayer P, Janning P, Thomashow LS, Mavrodi DV Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16431-6. Epub 2004 Nov 15. PMID:15545603<ref>PMID:15545603</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1sdj" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Edstrom, W]]	+	[[Category: Edstrom W]]
-	[[Category: Korniyenko, Y]]	+	[[Category: Korniyenko Y]]
-	[[Category: Kuzin~~, A P]]~~	+	[[Category: Kuzin AP]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Savchenko A]]
-	[[Category: Savchenko, A]]	+	[[Category: Skarina T]]
-	[[Category: Skarina, T]]	+	[[Category: Tong L]]
-	[[Category: Tong, L]]	+
-	~~[[Category: Nesg]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Unknown function~~]]	+

OCA at 13:46, 16 December 2020

OCA — Wed, 16 Dec 2020 13:46:12 GMT

←Older revision		Revision as of 13:46, 16 December 2020
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	==X-RAY STRUCTURE OF YDDE_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ET25.==		==X-RAY STRUCTURE OF YDDE_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ET25.==
-	<StructureSection load='1sdj' size='340' side='right' caption='[[1sdj]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='1sdj' size='340' side='right'caption='[[1sdj]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1sdj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1p9v 1p9v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SDJ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1SDJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1sdj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1p9v 1p9v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SDJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1SDJ 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p9v\|1p9v]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1p9v\|1p9v]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YDDE, B1464 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YDDE, B1464 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1sdj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sdj OCA], [http://pdbe.org/1sdj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sdj RCSB], [http://www.ebi.ac.uk/pdbsum/1sdj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sdj ProSAT], [http://www.topsan.org/Proteins/NESGC/1sdj TOPSAN]</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=1sdj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sdj OCA], [http://pdbe.org/1sdj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sdj RCSB], [http://www.ebi.ac.uk/pdbsum/1sdj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sdj ProSAT], [http://www.topsan.org/Proteins/NESGC/1sdj TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Edstrom, W]]		[[Category: Edstrom, W]]
	[[Category: Korniyenko, Y]]		[[Category: Korniyenko, Y]]

OCA at 06:48, 8 March 2018

OCA — Thu, 08 Mar 2018 06:48:44 GMT

←Older revision		Revision as of 06:48, 8 March 2018
Line 1:		Line 1:
		+
	==X-RAY STRUCTURE OF YDDE_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ET25.==		==X-RAY STRUCTURE OF YDDE_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ET25.==
	<StructureSection load='1sdj' size='340' side='right' caption='[[1sdj]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1sdj' size='340' side='right' caption='[[1sdj]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p9v\|1p9v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p9v\|1p9v]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YDDE, B1464 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YDDE, B1464 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sdj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sdj OCA], [http://pdbe.org/1sdj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sdj RCSB], [http://www.ebi.ac.uk/pdbsum/1sdj PDBsum], [http://www.topsan.org/Proteins/NESGC/1sdj TOPSAN]</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=1sdj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sdj OCA], [http://pdbe.org/1sdj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sdj RCSB], [http://www.ebi.ac.uk/pdbsum/1sdj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sdj ProSAT], [http://www.topsan.org/Proteins/NESGC/1sdj TOPSAN]</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/sd/1sdj_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sd/1sdj_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=1sdj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:41, 11 September 2015

OCA — Fri, 11 Sep 2015 13:41:57 GMT

←Older revision		Revision as of 13:41, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1sdj' size='340' side='right' caption='[[1sdj]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1sdj' size='340' side='right' caption='[[1sdj]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1sdj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1p9v 1p9v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SDJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SDJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1sdj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1p9v 1p9v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SDJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SDJ 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p9v\|1p9v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p9v\|1p9v]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YDDE, B1464 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YDDE, B1464 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sdj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sdj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sdj RCSB], [http://www.ebi.ac.uk/pdbsum/1sdj PDBsum], [http://www.topsan.org/Proteins/NESGC/1sdj TOPSAN]</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=1sdj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sdj OCA], [http://pdbe.org/1sdj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sdj RCSB], [http://www.ebi.ac.uk/pdbsum/1sdj PDBsum], [http://www.topsan.org/Proteins/NESGC/1sdj TOPSAN]</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 1sdj" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Edstrom, W]]		[[Category: Edstrom, W]]
	[[Category: Korniyenko, Y]]		[[Category: Korniyenko, Y]]

OCA at 17:13, 25 December 2014

OCA — Thu, 25 Dec 2014 17:13:18 GMT

←Older revision		Revision as of 17:13, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1sdj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1p9v 1p9v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SDJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SDJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1sdj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1p9v 1p9v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SDJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SDJ 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>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p9v\|1p9v]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p9v\|1p9v]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YDDE, B1464 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YDDE, B1464 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sdj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sdj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sdj RCSB], [http://www.ebi.ac.uk/pdbsum/1sdj PDBsum], [http://www.topsan.org/Proteins/NESGC/1sdj TOPSAN]</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=1sdj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sdj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sdj RCSB], [http://www.ebi.ac.uk/pdbsum/1sdj PDBsum], [http://www.topsan.org/Proteins/NESGC/1sdj TOPSAN]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Edstrom, W.]]	+	[[Category: Edstrom, W]]
-	[[Category: Korniyenko, Y.]]	+	[[Category: Korniyenko, Y]]
-	[[Category: Kuzin, A P~~.]]~~	+	[[Category: Kuzin, A P]]
-	~~[[Category: NESG, Northeast Structural Genomics Consortium.]]~~	+
-	~~[[Category: Savchenko, A.]]~~	+
-	~~[[Category: Skarina, T.]]~~	+
-	~~[[Category: Tong, L.]]~~	+
-	~~[[Category: Nesg]]~~	+
-	~~[[Category: Northeast structural genomics consortium]]~~	+
-	~~[[Category: Protein structure initiative]]~~	+
-	~~[[Category: Psi~~]]	+
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
		+	[[Category: Savchenko, A]]
		+	[[Category: Skarina, T]]
		+	[[Category: Tong, L]]
		+	[[Category: Nesg]]
		+	[[Category: PSI, Protein structure initiative]]
	[[Category: Unknown function]]		[[Category: Unknown function]]

OCA at 15:57, 29 September 2014

OCA — Mon, 29 Sep 2014 15:57:48 GMT

←Older revision		Revision as of 15:57, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1sdj.~~png~~\|~~left~~\|200px]]	+	==X-RAY STRUCTURE OF YDDE_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ET25.==
		+	<StructureSection load='1sdj' size='340' side='right' caption='[[1sdj]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1sdj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1p9v 1p9v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SDJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SDJ 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>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p9v\|1p9v]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YDDE, B1464 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sdj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sdj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sdj RCSB], [http://www.ebi.ac.uk/pdbsum/1sdj PDBsum], [http://www.topsan.org/Proteins/NESGC/1sdj TOPSAN]</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/sd/1sdj_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 ==
		+	Phenazines produced by Pseudomonas and Streptomyces spp. are heterocyclic nitrogen-containing metabolites with antibiotic, antitumor, and antiparasitic activity. The antibiotic properties of pyocyanin, produced by Pseudomonas aeruginosa, were recognized in the 1890s, although this blue phenazine is now known to be a virulence factor in human disease. Despite their biological significance, the biosynthesis of phenazines is not fully understood. Here we present structural and functional studies of PhzF, an enzyme essential for phenazine synthesis in Pseudomonas spp. PhzF shares topology with diaminopimelate epimerase DapF but lacks the same catalytic residues. The structure of PhzF in complex with its substrate, trans-2,3-dihydro-3-hydroxyanthranilic acid, suggests that it is an isomerase using the conserved glutamate E45 to abstract a proton from C3 of the substrate. The proton is returned to C1 of the substrate after rearrangement of the double-bond system, yielding an enol that converts to the corresponding ketone. PhzF is a dimer that may be bifunctional, providing a shielded cavity for ketone dimerization via double Schiff-base formation to produce the phenazine scaffold. Our proposed mechanism is supported by mass and NMR spectroscopy. The results are discussed in the context of related structures and protein sequences of unknown biochemical function.

-	~~{{STRUCTURE_1sdj\| PDB=1sdj \| SCENE= }}~~	+	Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens.,Blankenfeldt W, Kuzin AP, Skarina T, Korniyenko Y, Tong L, Bayer P, Janning P, Thomashow LS, Mavrodi DV Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16431-6. Epub 2004 Nov 15. PMID:15545603<ref>PMID:15545603</ref>

-	~~===X-RAY STRUCTURE OF YDDE_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ET25.===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15545603}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1sdj]] is~~ a ~~1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes~~ the ~~now removed PDB entry [http://oca~~.~~weizmann~~.ac.il/~~oca-bin/send-pdb?obs=1&id=1p9v 1p9v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SDJ OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015545603<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Edstrom, W.]]		[[Category: Edstrom, W.]]

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

OCA — Fri, 04 Jan 2013 10:16:10 GMT

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

←Older revision

Revision as of 10:16, 4 January 2013

OCA at 10:16, 4 January 2013

OCA — Fri, 04 Jan 2013 10:16:07 GMT

←Older revision		Revision as of 10:16, 4 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1sdj.png\|left\|200px]]		[[Image:1sdj.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1sdj", 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_1sdj\| PDB=1sdj \| SCENE= }}		{{STRUCTURE_1sdj\| PDB=1sdj \| SCENE= }}

	===X-RAY STRUCTURE OF YDDE_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ET25.===		===X-RAY STRUCTURE OF YDDE_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ET25.===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15545603}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15545603 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15545603}}		{{ABSTRACT_PUBMED_15545603}}

	==About this Structure==		==About this Structure==
-	~~1SDJ~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1p9v 1p9v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SDJ OCA].	+	[[1sdj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1p9v 1p9v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SDJ OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15545603~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015545603</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Edstrom, W.]]		[[Category: Edstrom, W.]]
Line 38:		Line 26:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Unknown function]]		[[Category: Unknown function]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 23:52:15 2009''

OCA at 21:52, 17 February 2009

OCA — Tue, 17 Feb 2009 21:52:15 GMT

←Older revision		Revision as of 21:52, 17 February 2009
Line 23:		Line 23:

	==Reference==		==Reference==
-	Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens., Blankenfeldt W, Kuzin AP, Skarina T, Korniyenko Y, Tong L, Bayer P, Janning P, Thomashow LS, Mavrodi DV, Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16431-6. Epub 2004 Nov 15. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15545603 15545603]~~	+	<ref group="xtra">PMID:15545603</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Edstrom, W.]]		[[Category: Edstrom, W.]]
Line 39:		Line 39:
	[[Category: Unknown function]]		[[Category: Unknown function]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Nov 16 15~~:03:~~33 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 23:52:15 2009''

OCA at 13:03, 16 November 2008

OCA — Sun, 16 Nov 2008 13:03:34 GMT

←Older revision		Revision as of 13:03, 16 November 2008
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1SDJ is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1p9v 1p9v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SDJ OCA].	+	1SDJ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1p9v 1p9v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SDJ OCA].

	==Reference==		==Reference==
	Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens., Blankenfeldt W, Kuzin AP, Skarina T, Korniyenko Y, Tong L, Bayer P, Janning P, Thomashow LS, Mavrodi DV, Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16431-6. Epub 2004 Nov 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15545603 15545603]		Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens., Blankenfeldt W, Kuzin AP, Skarina T, Korniyenko Y, Tong L, Bayer P, Janning P, Thomashow LS, Mavrodi DV, Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16431-6. Epub 2004 Nov 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15545603 15545603]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Edstrom, W.]]		[[Category: Edstrom, W.]]
	[[Category: Korniyenko, Y.]]		[[Category: Korniyenko, Y.]]
Line 40:		Line 39:
	[[Category: Unknown function]]		[[Category: Unknown function]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 07~~:08:44 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Nov 16 15:03:33 2008''