4jip - Revision history

OCA at 15:43, 20 September 2023

OCA — Wed, 20 Sep 2023 15:43:46 GMT

←Older revision		Revision as of 15:43, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4jip]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JIP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JIP FirstGlance]. <br>		<table><tr><td colspan='2'>[[4jip]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JIP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JIP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=HBA:P-HYDROXYBENZALDEHYDE'>HBA</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]] 2.29Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=HBA:P-HYDROXYBENZALDEHYDE'>HBA</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=4jip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jip OCA], [https://pdbe.org/4jip PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jip RCSB], [https://www.ebi.ac.uk/pdbsum/4jip PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jip 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=4jip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jip OCA], [https://pdbe.org/4jip PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jip RCSB], [https://www.ebi.ac.uk/pdbsum/4jip PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jip ProSAT]</span></td></tr>
	</table>		</table>

OCA at 11:15, 24 November 2022

OCA — Thu, 24 Nov 2022 11:15:17 GMT

←Older revision		Revision as of 11:15, 24 November 2022
Line 1:		Line 1:

	==Crystal structure of glycerol trinitrate reductase NerA from Agrobacterium radiobacter in complex with 4-hydroxybenzaldehyde==		==Crystal structure of glycerol trinitrate reductase NerA from Agrobacterium radiobacter in complex with 4-hydroxybenzaldehyde==
-	<StructureSection load='4jip' size='340' side='right' caption='[[4jip]], [[Resolution\|resolution]] 2.29Å' scene=''>	+	<StructureSection load='4jip' size='340' side='right'caption='[[4jip]], [[Resolution\|resolution]] 2.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4jip]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JIP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4JIP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4jip]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JIP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JIP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=HBA:P-HYDROXYBENZALDEHYDE'>HBA</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=HBA:P-HYDROXYBENZALDEHYDE'>HBA</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jic\|4jic]], [[4jiq\|4jiq]]</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=4jip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jip OCA], [https://pdbe.org/4jip PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jip RCSB], [https://www.ebi.ac.uk/pdbsum/4jip PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jip ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nerA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 "Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934])</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=4jip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jip OCA], [~~http~~://pdbe.org/4jip PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4jip RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4jip PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4jip ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O31246_RHIRD O31246_RHIRD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Gruber, K~~]]	+	[[Category: Agrobacterium tumefaciens]]
-	[[Category: ~~Oberdorfer, G~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Ene-reductase~~]]	+	[[Category: Gruber K]]
-	[[Category: ~~Oxidoreductase]]~~	+	[[Category: Oberdorfer G]]
-	~~[[Category: Tim-barrel~~]]	+

OCA at 12:05, 11 August 2016

OCA — Thu, 11 Aug 2016 12:05:48 GMT

←Older revision		Revision as of 12:05, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of glycerol trinitrate reductase NerA from Agrobacterium radiobacter in complex with 4-hydroxybenzaldehyde==		==Crystal structure of glycerol trinitrate reductase NerA from Agrobacterium radiobacter in complex with 4-hydroxybenzaldehyde==
	<StructureSection load='4jip' size='340' side='right' caption='[[4jip]], [[Resolution\|resolution]] 2.29Å' scene=''>		<StructureSection load='4jip' size='340' side='right' caption='[[4jip]], [[Resolution\|resolution]] 2.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4jip]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Agrobacterium_tumefaciens Agrobacterium tumefaciens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JIP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JIP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4jip]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JIP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JIP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=HBA:P-HYDROXYBENZALDEHYDE'>HBA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=HBA:P-HYDROXYBENZALDEHYDE'>HBA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jic\|4jic]], [[4jiq\|4jiq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jic\|4jic]], [[4jiq\|4jiq]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nerA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 ~~Agrobacterium tumefaciens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nerA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 "Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934])</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=4jip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jip OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jip RCSB], [http://www.ebi.ac.uk/pdbsum/4jip 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=4jip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jip OCA], [http://pdbe.org/4jip PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jip RCSB], [http://www.ebi.ac.uk/pdbsum/4jip PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jip ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4jip" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Agrobacterium tumefaciens]]
	[[Category: Gruber, K]]		[[Category: Gruber, K]]
	[[Category: Oberdorfer, G]]		[[Category: Oberdorfer, G]]

OCA at 06:35, 22 January 2015

OCA — Thu, 22 Jan 2015 06:35:37 GMT

←Older revision		Revision as of 06:35, 22 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4jip\| PDB=4jip \| SCENE= }}~~	+	==Crystal structure of glycerol trinitrate reductase NerA from Agrobacterium radiobacter in complex with 4-hydroxybenzaldehyde==
-	===Crystal structure of glycerol trinitrate reductase NerA from Agrobacterium radiobacter in complex with 4-hydroxybenzaldehyde===	+	<StructureSection load='4jip' size='340' side='right' caption='[[4jip]], [[Resolution\|resolution]] 2.29Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23606302}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4jip]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JIP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JIP FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=HBA:P-HYDROXYBENZALDEHYDE'>HBA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jic\|4jic]], [[4jiq\|4jiq]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nerA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 Agrobacterium tumefaciens])</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=4jip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jip OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jip RCSB], [http://www.ebi.ac.uk/pdbsum/4jip PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In recent years, Old Yellow Enzymes (OYEs) and their homologues have found broad application in the efficient asymmetric hydrogenation of activated CC bonds with high selectivities and yields. Members of this class of enzymes have been found in many different organisms and are rather diverse on the sequence level, with pairwise identities as low as 20 %, but they exhibit significant structural similarities with the adoption of a conserved (alphabeta)8 -barrel fold. Some OYEs have been shown not only to reduce CC double bonds, but also to be capable of reducing nitro groups in both saturated and unsaturated substrates. In order to understand this dual activity we determined and analyzed X-ray crystal structures of NerA from Agrobacterium radiobacter, both in its apo form and in complex with 4-hydroxybenzaldehyde and with 1-nitro-2-phenylpropene. These structures, together with spectroscopic studies of substrate binding to several OYEs, indicate that nitro-containing substrates can bind to OYEs in different binding modes, one of which leads to CC double bond reduction and the other to nitro group reduction.

-	~~==About this~~ Structure==	+	The Structure of Glycerol Trinitrate Reductase NerA from Agrobacterium radiobacter Reveals the Molecular Reason for Nitro- and Ene-Reductase Activity in OYE Homologues.,Oberdorfer G, Binter A, Wallner S, Durchschein K, Hall M, Faber K, Macheroux P, Gruber K Chembiochem. 2013 May 10;14(7):836-45. doi: 10.1002/cbic.201300136. Epub 2013 Apr, 18. PMID:23606302<ref>PMID:23606302</ref>
-	~~[[4jip]] is a 1 chain structure with sequence~~ from ~~[http~~:~~//en~~.~~wikipedia~~.~~org/wiki~~/~~Agrobacterium_tumefaciens Agrobacterium tumefaciens]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id~~=~~4JIP OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Agrobacterium tumefaciens]]		[[Category: Agrobacterium tumefaciens]]
-	[[Category: Gruber, K.]]	+	[[Category: Gruber, K]]
-	[[Category: Oberdorfer, G.]]	+	[[Category: Oberdorfer, G]]
	[[Category: Ene-reductase]]		[[Category: Ene-reductase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Tim-barrel]]		[[Category: Tim-barrel]]

OCA at 07:45, 8 May 2013

OCA — Wed, 08 May 2013 07:45:50 GMT

←Older revision		Revision as of 07:45, 8 May 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4jip\| PDB=4jip \| SCENE= }}
		+	===Crystal structure of glycerol trinitrate reductase NerA from Agrobacterium radiobacter in complex with 4-hydroxybenzaldehyde===
		+	{{ABSTRACT_PUBMED_23606302}}

-	~~The entry~~ 4jip is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4jip]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JIP OCA].
-	~~Authors~~: ~~Oberdorfer, G.,~~ Gruber, K.	+	[[Category: Agrobacterium tumefaciens]]
-		+	[[Category: Gruber, K.]]
-	~~Description~~: ~~Crystal structure of glycerol trinitrate~~ reductase ~~NerA from Agrobacterium radiobacter in complex with 4~~-~~hydroxybenzaldehyde~~	+	[[Category: Oberdorfer, G.]]
		+	[[Category: Ene-reductase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Tim-barrel]]

OCA at 19:54, 17 April 2013

OCA — Wed, 17 Apr 2013 19:54:45 GMT

←Older revision		Revision as of 19:54, 17 April 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4jip is ON HOLD	+	The entry 4jip is ON HOLD until Paper Publication

	Authors: Oberdorfer, G., Gruber, K.		Authors: Oberdorfer, G., Gruber, K.

	Description: Crystal structure of glycerol trinitrate reductase NerA from Agrobacterium radiobacter in complex with 4-hydroxybenzaldehyde		Description: Crystal structure of glycerol trinitrate reductase NerA from Agrobacterium radiobacter in complex with 4-hydroxybenzaldehyde

OCA at 16:20, 20 March 2013

OCA — Wed, 20 Mar 2013 16:20:11 GMT

←Older revision		Revision as of 16:20, 20 March 2013
Line 3:		Line 3:
	The entry 4jip is ON HOLD		The entry 4jip is ON HOLD

-	Authors: Oberdorfer, G, Gruber, K	+	Authors: Oberdorfer, G., Gruber, K.

	Description: Crystal structure of glycerol trinitrate reductase NerA from Agrobacterium radiobacter in complex with 4-hydroxybenzaldehyde		Description: Crystal structure of glycerol trinitrate reductase NerA from Agrobacterium radiobacter in complex with 4-hydroxybenzaldehyde

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

OCA — Wed, 13 Mar 2013 10:03:09 GMT

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

←Older revision

Revision as of 10:03, 13 March 2013

OCA: New page: '''Unreleased structure''' The entry 4jip is ON HOLD Authors: Oberdorfer, G, Gruber, K Description: Crystal structure of glycerol trinitrate reductase NerA from Agrobacterium radiobact...

OCA — Wed, 13 Mar 2013 10:03:08 GMT

New page: '''Unreleased structure''' The entry 4jip is ON HOLD Authors: Oberdorfer, G, Gruber, K Description: Crystal structure of glycerol trinitrate reductase NerA from Agrobacterium radiobact...

New page

'''Unreleased structure'''

The entry 4jip is ON HOLD

Authors: Oberdorfer, G, Gruber, K

Description: Crystal structure of glycerol trinitrate reductase NerA from Agrobacterium radiobacter in complex with 4-hydroxybenzaldehyde