4o94 - Revision history

OCA at 07:12, 25 January 2023

OCA — Wed, 25 Jan 2023 07:12:31 GMT

←Older revision		Revision as of 07:12, 25 January 2023
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	==Crystal structure of a trap periplasmic solute binding protein from Rhodopseudomonas palustris HaA2 (RPB_3329), Target EFI-510223, with bound succinate==		==Crystal structure of a trap periplasmic solute binding protein from Rhodopseudomonas palustris HaA2 (RPB_3329), Target EFI-510223, with bound succinate==
-	<StructureSection load='4o94' size='340' side='right' caption='[[4o94]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='4o94' size='340' side='right'caption='[[4o94]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4o94]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Rhop2 Rhop2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O94 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4O94 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4o94]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodopseudomonas_palustris_HaA2 Rhodopseudomonas palustris HaA2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O94 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O94 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=~~SIN~~:~~SUCCINIC+ACID~~'>~~SIN~~</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4o94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o94 OCA], [https://pdbe.org/4o94 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o94 RCSB], [https://www.ebi.ac.uk/pdbsum/4o94 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o94 ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RPB_3329 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316058 RHOP2])~~</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=4o94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o94 OCA], [~~http~~://pdbe.org/4o94 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4o94 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4o94 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4o94 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q2IUT5_RHOP2 Q2IUT5_RHOP2]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 4o94" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4o94" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[TRAP dicarboxylate transporter%2C DctP subunit\|TRAP dicarboxylate transporter%2C DctP subunit]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rhop2~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Almo, S C~~]]	+	[[Category: Rhodopseudomonas palustris HaA2]]
-	[[Category: ~~Attonito, J D~~]]	+	[[Category: Al Obaidi NF]]
-	[[Category: ~~Chowdhury, S~~]]	+	[[Category: Almo SC]]
-	[[Category: ~~EFI, Enzyme Function Initiative~~]]	+	[[Category: Attonito JD]]
-	[[Category: ~~Evans, B~~]]	+	[[Category: Chowdhury S]]
-	[[Category: ~~Gerlt, J A~~]]	+	[[Category: Evans B]]
-	[[Category: ~~Glenn, A Scott~~]]	+	[[Category: Gerlt JA]]
-	[[Category: Hillerich, B]]	+	[[Category: Hillerich B]]
-	[[Category: Imker~~, H J~~]]	+	[[Category: Imker HJ]]
-	[[Category: Love, J]]	+	[[Category: Love J]]
-	[[Category: Morisco~~, L L~~]]	+	[[Category: Morisco LL]]
-	[[Category: ~~Obaidi, N F.Al~~]]	+	[[Category: Scott Glenn A]]
-	[[Category: Seidel~~, R D~~]]	+	[[Category: Seidel RD]]
-	[[Category: Sojitra, S]]	+	[[Category: Sojitra S]]
-	[[Category: Stead, M]]	+	[[Category: Stead M]]
-	[[Category: Vetting~~, M W~~]]	+	[[Category: Vetting MW]]
-	[[Category: Wasserman~~, S R]]~~	+	[[Category: Wasserman SR]]
-	~~[[Category: Efi]]~~	+
-	~~[[Category: Enzyme function initiative]]~~	+
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Transport protein]]~~	+
-	~~[[Category: Trap periplasmic solute binding family~~]]	+

OCA at 16:55, 2 January 2017

OCA — Mon, 02 Jan 2017 16:55:20 GMT

←Older revision		Revision as of 16:55, 2 January 2017
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		+
	==Crystal structure of a trap periplasmic solute binding protein from Rhodopseudomonas palustris HaA2 (RPB_3329), Target EFI-510223, with bound succinate==		==Crystal structure of a trap periplasmic solute binding protein from Rhodopseudomonas palustris HaA2 (RPB_3329), Target EFI-510223, with bound succinate==
	<StructureSection load='4o94' size='340' side='right' caption='[[4o94]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='4o94' size='340' side='right' caption='[[4o94]], [[Resolution\|resolution]] 2.00Å' scene=''>
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	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RPB_3329 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316058 RHOP2])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RPB_3329 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316058 RHOP2])</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=4o94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o94 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o94 RCSB], [http://www.ebi.ac.uk/pdbsum/4o94 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=4o94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o94 OCA], [http://pdbe.org/4o94 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4o94 RCSB], [http://www.ebi.ac.uk/pdbsum/4o94 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4o94 ProSAT]</span></td></tr>
	</table>		</table>
	<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 4o94" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:57, 25 February 2015

OCA — Wed, 25 Feb 2015 07:57:36 GMT

←Older revision		Revision as of 07:57, 25 February 2015
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	<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=4o94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o94 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o94 RCSB], [http://www.ebi.ac.uk/pdbsum/4o94 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=4o94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o94 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o94 RCSB], [http://www.ebi.ac.uk/pdbsum/4o94 PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The rate at which genome sequencing data is accruing demands enhanced methods for functional annotation and metabolism discovery. Solute binding proteins (SBPs) facilitate the transport of the first reactant in a metabolic pathway, thereby constraining the regions of chemical space and the chemistries that must be considered for pathway reconstruction. We describe high-throughput protein production and differential scanning fluorimetry platforms, which enabled the screening of 158 SBPs against a 189 component library specifically tailored for this class of proteins. Like all screening efforts, this approach is limited by the practical constraints imposed by construction of the library, i.e., we can study only those metabolites that are known to exist and which can be made in sufficient quantities for experimentation. To move beyond these inherent limitations, we illustrate the promise of crystallographic- and mass spectrometric-based approaches for the unbiased use of entire metabolomes as screening libraries. Together, our approaches identified 40 new SBP ligands, generated experiment-based annotations for 2084 SBPs in 71 isofunctional clusters, and defined numerous metabolic pathways, including novel catabolic pathways for the utilization of ethanolamine as sole nitrogen source and the use of d-Ala-d-Ala as sole carbon source. These efforts begin to define an integrated strategy for realizing the full value of amassing genome sequence data.
		+
		+	Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.,Vetting MW, Al-Obaidi N, Zhao S, San Francisco B, Kim J, Wichelecki DJ, Bouvier JT, Solbiati JO, Vu H, Zhang X, Rodionov DA, Love JD, Hillerich BS, Seidel RD, Quinn RJ, Osterman AL, Cronan JE, Jacobson MP, Gerlt JA, Almo SC Biochemistry. 2015 Jan 27;54(3):909-31. doi: 10.1021/bi501388y. Epub 2015 Jan 16. PMID:25540822<ref>PMID:25540822</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 09:15, 5 January 2015

OCA — Mon, 05 Jan 2015 09:15:00 GMT

←Older revision		Revision as of 09:15, 5 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4o94\| PDB=4o94 \| SCENE= }}~~	+	==Crystal structure of a trap periplasmic solute binding protein from Rhodopseudomonas palustris HaA2 (RPB_3329), Target EFI-510223, with bound succinate==
-	===Crystal structure of a trap periplasmic solute binding protein from Rhodopseudomonas palustris HaA2 (RPB_3329), Target EFI-510223, with bound succinate===	+	<StructureSection load='4o94' size='340' side='right' caption='[[4o94]], [[Resolution\|resolution]] 2.00Å' scene=''>
-		+	== Structural highlights ==
-	==~~About this Structure~~==	+	<table><tr><td colspan='2'>[[4o94]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhop2 Rhop2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O94 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O94 FirstGlance]. <br>
-	[[4o94]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O94 OCA].	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>
-	[[Category: Almo, S C.]]	+	<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>
-	[[Category: Attonito, J D.]]	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RPB_3329 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316058 RHOP2])</td></tr>
-	[[Category: Chowdhury, S.]]	+	<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=4o94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o94 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o94 RCSB], [http://www.ebi.ac.uk/pdbsum/4o94 PDBsum]</span></td></tr>
-	[[Category: EFI, Enzyme Function Initiative.]]	+	</table>
-	[[Category: Evans, B.]]	+	__TOC__
-	[[Category: Gerlt, J A.]]	+	</StructureSection>
-	[[Category: Glenn, A Scott.]]	+	[[Category: Rhop2]]
-	[[Category: Hillerich, B.]]	+	[[Category: Almo, S C]]
-	[[Category: Imker, H J.]]	+	[[Category: Attonito, J D]]
-	[[Category: Love, J.]]	+	[[Category: Chowdhury, S]]
-	[[Category: Morisco, L L.]]	+	[[Category: EFI, Enzyme Function Initiative]]
-	[[Category: Obaidi, N F.Al.]]	+	[[Category: Evans, B]]
-	[[Category: Seidel, R D.]]	+	[[Category: Gerlt, J A]]
-	[[Category: Sojitra, S.]]	+	[[Category: Glenn, A Scott]]
-	[[Category: Stead, M.]]	+	[[Category: Hillerich, B]]
-	[[Category: Vetting, M W.]]	+	[[Category: Imker, H J]]
-	[[Category: Wasserman, S R.]]	+	[[Category: Love, J]]
		+	[[Category: Morisco, L L]]
		+	[[Category: Obaidi, N F.Al]]
		+	[[Category: Seidel, R D]]
		+	[[Category: Sojitra, S]]
		+	[[Category: Stead, M]]
		+	[[Category: Vetting, M W]]
		+	[[Category: Wasserman, S R]]
	[[Category: Efi]]		[[Category: Efi]]
	[[Category: Enzyme function initiative]]		[[Category: Enzyme function initiative]]

OCA at 07:06, 22 January 2014

OCA — Wed, 22 Jan 2014 07:06:20 GMT

←Older revision		Revision as of 07:06, 22 January 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4o94\| PDB=4o94 \| SCENE= }}
		+	===Crystal structure of a trap periplasmic solute binding protein from Rhodopseudomonas palustris HaA2 (RPB_3329), Target EFI-510223, with bound succinate===

-	~~The entry~~ 4o94 is ~~ON HOLD~~	+	==About this Structure==
-		+	[[4o94]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O94 OCA].
-	~~Authors~~: ~~Vetting, M~~.W.~~, Al Obaidi, N~~.F.~~, Morisco, L.L., Wasserman~~, S.~~R., Sojitra, S., Stead, M.,~~ Attonito, J.D.~~, Scott Glenn, A.,~~ Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., ~~Imker, H.J~~., ~~Gerlt~~, ~~J.A~~.~~, Almo~~, S.~~C.,~~ Enzyme ~~Function Initiative (EFI)~~	+	[[Category: Almo, S C.]]
-		+	[[Category: Attonito, J D.]]
-	~~Description~~: ~~Crystal structure of a trap~~ periplasmic solute binding ~~protein from Rhodopseudomonas palustris HaA2 (RPB_3329), Target EFI-510223, with bound succinate~~	+	[[Category: Chowdhury, S.]]
		+	[[Category: EFI, Enzyme Function Initiative.]]
		+	[[Category: Evans, B.]]
		+	[[Category: Gerlt, J A.]]
		+	[[Category: Glenn, A Scott.]]
		+	[[Category: Hillerich, B.]]
		+	[[Category: Imker, H J.]]
		+	[[Category: Love, J.]]
		+	[[Category: Morisco, L L.]]
		+	[[Category: Obaidi, N F.Al.]]
		+	[[Category: Seidel, R D.]]
		+	[[Category: Sojitra, S.]]
		+	[[Category: Stead, M.]]
		+	[[Category: Vetting, M W.]]
		+	[[Category: Wasserman, S R.]]
		+	[[Category: Efi]]
		+	[[Category: Enzyme function initiative]]
		+	[[Category: Structural genomic]]
		+	[[Category: Transport protein]]
		+	[[Category: Trap periplasmic solute binding family]]

OCA: Protected "4o94" [edit=sysop:move=sysop]

OCA — Wed, 08 Jan 2014 09:29:05 GMT

Protected "4o94" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:29, 8 January 2014

OCA: New page: '''Unreleased structure''' The entry 4o94 is ON HOLD Authors: Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Attonito, J.D., Scott Glenn, A., Ch...

OCA — Wed, 08 Jan 2014 09:29:03 GMT

New page: '''Unreleased structure''' The entry 4o94 is ON HOLD Authors: Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Attonito, J.D., Scott Glenn, A., Ch...

New page

'''Unreleased structure'''

The entry 4o94 is ON HOLD

Authors: Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Description: Crystal structure of a trap periplasmic solute binding protein from Rhodopseudomonas palustris HaA2 (RPB_3329), Target EFI-510223, with bound succinate