4i1d - Revision history

OCA at 08:33, 9 November 2022

OCA — Wed, 09 Nov 2022 08:33:55 GMT

←Older revision		Revision as of 08:33, 9 November 2022
Line 1:		Line 1:

	==The crystal structure of an ABC transporter substrate-binding protein from Bradyrhizobium japonicum USDA 110==		==The crystal structure of an ABC transporter substrate-binding protein from Bradyrhizobium japonicum USDA 110==
-	<StructureSection load='4i1d' size='340' side='right' caption='[[4i1d]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='4i1d' size='340' side='right'caption='[[4i1d]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4i1d]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bradu Bradu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I1D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4I1D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4i1d]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bradyrhizobium_diazoefficiens_USDA_110 Bradyrhizobium diazoefficiens USDA 110]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I1D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLT:D-MALATE'>MLT</scene>, <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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLT:D-MALATE'>MLT</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4i1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i1d OCA], [https://pdbe.org/4i1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i1d RCSB], [https://www.ebi.ac.uk/pdbsum/4i1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i1d ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fcl\|4fcl]]</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bll6825 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224911 BRADU])~~</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=4i1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i1d OCA], [~~http~~://pdbe.org/4i1d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4i1d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4i1d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4i1d ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q89F76_BRADU Q89F76_BRADU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bradu~~]]	+	[[Category: Bradyrhizobium diazoefficiens USDA 110]]
-	[[Category: ~~Collart, F~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Fan, Y~~]]	+	[[Category: Collart F]]
-	[[Category: ~~Joachimiak, A~~]]	+	[[Category: Fan Y]]
-	[[Category: ~~Structural genomic~~]]	+	[[Category: Joachimiak A]]
-	[[Category: Mack, J]]	+	[[Category: Mack J]]
-	[[Category: Tan, K]]	+	[[Category: Tan K]]
-	[[Category: Zerbs, S]]	+	[[Category: Zerbs S]]
-	~~[[Category: Mcsg]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Psi-biology]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 12:23, 4 August 2016

OCA — Thu, 04 Aug 2016 12:23:45 GMT

←Older revision		Revision as of 12:23, 4 August 2016
Line 1:		Line 1:
		+
	==The crystal structure of an ABC transporter substrate-binding protein from Bradyrhizobium japonicum USDA 110==		==The crystal structure of an ABC transporter substrate-binding protein from Bradyrhizobium japonicum USDA 110==
	<StructureSection load='4i1d' size='340' side='right' caption='[[4i1d]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='4i1d' size='340' side='right' caption='[[4i1d]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4i1d]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bradyrhizobium_diazoefficiens_usda_110 Bradyrhizobium diazoefficiens usda 110~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I1D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4i1d]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bradu Bradu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I1D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLT:D-MALATE'>MLT</scene>, <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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLT:D-MALATE'>MLT</scene>, <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">[[4fcl\|4fcl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fcl\|4fcl]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bll6825 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224911 ~~Bradyrhizobium diazoefficiens USDA 110~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bll6825 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224911 BRADU])</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=4i1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i1d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i1d RCSB], [http://www.ebi.ac.uk/pdbsum/4i1d 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=4i1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i1d OCA], [http://pdbe.org/4i1d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4i1d RCSB], [http://www.ebi.ac.uk/pdbsum/4i1d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4i1d ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	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 4i1d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bradyrhizobium diazoefficiens usda 110~~]]	+	[[Category: Bradu]]
	[[Category: Collart, F]]		[[Category: Collart, F]]
	[[Category: Fan, Y]]		[[Category: Fan, Y]]

OCA at 12:25, 21 December 2014

OCA — Sun, 21 Dec 2014 12:25:14 GMT

←Older revision		Revision as of 12:25, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4i1d\| PDB=4i1d \| SCENE= }}~~	+	==The crystal structure of an ABC transporter substrate-binding protein from Bradyrhizobium japonicum USDA 110==
-	===The crystal structure of an ABC transporter substrate-binding protein from Bradyrhizobium japonicum USDA 110===	+	<StructureSection load='4i1d' size='340' side='right' caption='[[4i1d]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23606130}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4i1d]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_diazoefficiens_usda_110 Bradyrhizobium diazoefficiens usda 110]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I1D FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLT:D-MALATE'>MLT</scene>, <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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fcl\|4fcl]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bll6825 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224911 Bradyrhizobium diazoefficiens USDA 110])</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=4i1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i1d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i1d RCSB], [http://www.ebi.ac.uk/pdbsum/4i1d PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Lignin comprises 15-25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP-binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p-coumarate, 3-phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X-ray crystal structures of protein-ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin-derived aromatic compounds. The screens and structural data provide new functional assignments for these solute-binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence-based functional annotation methods for this family of proteins. (c) Proteins 2013;. (c) 2013 Wiley Periodicals, Inc.

-	~~==About this Structure==~~	+	Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids.,Tan K, Chang C, Cuff M, Osipiuk J, Landorf E, Mack JC, Zerbs S, Joachimiak A, Collart FR Proteins. 2013 Apr 22. doi: 10.1002/prot.24305. PMID:23606130<ref>PMID:23606130</ref>
-	~~[[4i1d]] is a 4 chain structure with sequence~~ from ~~[http~~:~~//en~~.~~wikipedia~~.~~org/wiki/Bradyrhizobium_diazoefficiens_usda_110 Bradyrhizobium diazoefficiens usda 110]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4I1D OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023606130</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Bradyrhizobium diazoefficiens usda 110]]		[[Category: Bradyrhizobium diazoefficiens usda 110]]
-	[[Category: Collart, F.]]	+	[[Category: Collart, F]]
-	[[Category: Fan, Y.]]	+	[[Category: Fan, Y]]
-	[[Category: Joachimiak, A.]]	+	[[Category: Joachimiak, A]]
-	[[Category: ~~MCSG, Midwest Center for~~ Structural ~~Genomics.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Mack, J.]]	+	[[Category: Mack, J]]
-	[[Category: Tan, K.]]	+	[[Category: Tan, K]]
-	[[Category: Zerbs, S.]]	+	[[Category: Zerbs, S]]
	[[Category: Mcsg]]		[[Category: Mcsg]]
-	[[Category: ~~Midwest center for structural genomic]]~~	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category:~~ Protein structure initiative]]	+
	[[Category: Psi-biology]]		[[Category: Psi-biology]]
-	[[Category: Structural genomic]]
	[[Category: Transport protein]]		[[Category: Transport protein]]

OCA at 06:30, 29 September 2013

OCA — Sun, 29 Sep 2013 06:30:46 GMT

←Older revision		Revision as of 06:30, 29 September 2013
Line 4:		Line 4:

	==About this Structure==		==About this Structure==
-	[[4i1d]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bradyrhizobium_japonicum_usda_110~~ Bradyrhizobium ~~japonicum~~ usda 110]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I1D OCA].	+	[[4i1d]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_diazoefficiens_usda_110 Bradyrhizobium diazoefficiens usda 110]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I1D OCA].
-	[[Category: Bradyrhizobium ~~japonicum~~ usda 110]]	+
		+	==Reference==
		+	<ref group="xtra">PMID:023606130</ref><references group="xtra"/><references/>
		+	[[Category: Bradyrhizobium diazoefficiens usda 110]]
	[[Category: Collart, F.]]		[[Category: Collart, F.]]
	[[Category: Fan, Y.]]		[[Category: Fan, Y.]]

OCA at 06:08, 16 May 2013

OCA — Thu, 16 May 2013 06:08:58 GMT

←Older revision		Revision as of 06:08, 16 May 2013
Line 1:		Line 1:
-	[[Image:4i1d.jpg\|left\|200px]]
-
	{{STRUCTURE_4i1d\| PDB=4i1d \| SCENE= }}		{{STRUCTURE_4i1d\| PDB=4i1d \| SCENE= }}
-
	===The crystal structure of an ABC transporter substrate-binding protein from Bradyrhizobium japonicum USDA 110===		===The crystal structure of an ABC transporter substrate-binding protein from Bradyrhizobium japonicum USDA 110===
-		+	{{ABSTRACT_PUBMED_23606130}}

	==About this Structure==		==About this Structure==

OCA at 11:02, 5 December 2012

OCA — Wed, 05 Dec 2012 11:02:53 GMT

←Older revision		Revision as of 11:02, 5 December 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4i1d.jpg\|left\|200px]]

-	~~The entry~~ 4i1d ~~is ON HOLD~~	+	{{STRUCTURE_4i1d\| PDB=4i1d \| SCENE= }}

-	~~Authors: Fan, Y., Tan, K., Mack, J., Zerbs, S., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)~~	+	===The crystal structure of an ABC transporter substrate-binding protein from Bradyrhizobium japonicum USDA 110===

-	~~Description: The crystal~~ structure ~~of an ABC transporter substrate-binding protein~~ from Bradyrhizobium japonicum ~~USDA~~ 110	+
		+	==About this Structure==
		+	[[4i1d]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum_usda_110 Bradyrhizobium japonicum usda 110]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I1D OCA].
		+	[[Category: Bradyrhizobium japonicum usda 110]]
		+	[[Category: Collart, F.]]
		+	[[Category: Fan, Y.]]
		+	[[Category: Joachimiak, A.]]
		+	[[Category: MCSG, Midwest Center for Structural Genomics.]]
		+	[[Category: Mack, J.]]
		+	[[Category: Tan, K.]]
		+	[[Category: Zerbs, S.]]
		+	[[Category: Mcsg]]
		+	[[Category: Midwest center for structural genomic]]
		+	[[Category: Protein structure initiative]]
		+	[[Category: Psi-biology]]
		+	[[Category: Structural genomic]]
		+	[[Category: Transport protein]]

OCA: Protected "4i1d" [edit=sysop:move=sysop]

OCA — Wed, 28 Nov 2012 14:07:12 GMT

Protected "4i1d" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:07, 28 November 2012

OCA: New page: '''Unreleased structure''' The entry 4i1d is ON HOLD Authors: Fan, Y., Tan, K., Mack, J., Zerbs, S., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG) Descript...

OCA — Wed, 28 Nov 2012 14:07:11 GMT

New page: '''Unreleased structure''' The entry 4i1d is ON HOLD Authors: Fan, Y., Tan, K., Mack, J., Zerbs, S., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG) Descript...

New page

'''Unreleased structure'''

The entry 4i1d is ON HOLD

Authors: Fan, Y., Tan, K., Mack, J., Zerbs, S., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Description: The crystal structure of an ABC transporter substrate-binding protein from Bradyrhizobium japonicum USDA 110