3bm1 - Revision history

OCA at 14:48, 1 November 2023

OCA — Wed, 01 Nov 2023 14:48:04 GMT

←Older revision		Revision as of 14:48, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='3bm1' size='340' side='right'caption='[[3bm1]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3bm1' size='340' side='right'caption='[[3bm1]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bm1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BM1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bm1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BM1 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></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]] 2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3bm2\|3bm2]]</div>~~</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></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ydjA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~83333 ECOLI])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/6,7-dihydropteridine_reductase 6,7-dihydropteridine reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.34 1.5.1.34]~~ </~~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=3bm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm1 OCA], [https://pdbe.org/3bm1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bm1 RCSB], [https://www.ebi.ac.uk/pdbsum/3bm1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bm1 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=3bm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm1 OCA], [https://pdbe.org/3bm1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bm1 RCSB], [https://www.ebi.ac.uk/pdbsum/3bm1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bm1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/YDJA_ECOLI YDJA_ECOLI]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Nitroreductase\|Nitroreductase]]	+	*[[Nitroreductase 3D structures\|Nitroreductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~6,7~~-~~dihydropteridine reductase]]~~	+	[[Category: Escherichia coli K-12]]
-	~~[[Category: Ecoli~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Choi~~, J W~~]]	+	[[Category: Choi JW]]
-	[[Category: Kim~~, J S]]~~	+	[[Category: Kim JS]]
-	~~[[Category: Nitroreductase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Ydja~~]]	+

OCA at 08:19, 19 January 2022

OCA — Wed, 19 Jan 2022 08:19:09 GMT

←Older revision		Revision as of 08:19, 19 January 2022
Line 1:		Line 1:

	==Crystal structure of a minimal nitroreductase ydjA from Escherichia coli K12 with and without FMN cofactor==		==Crystal structure of a minimal nitroreductase ydjA from Escherichia coli K12 with and without FMN cofactor==
-	<StructureSection load='3bm1' size='340' side='right' caption='[[3bm1]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='3bm1' size='340' side='right'caption='[[3bm1]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bm1]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3BM1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bm1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BM1 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></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></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bm2\|3bm2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3bm2\|3bm2]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ydjA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ydjA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/6,7-dihydropteridine_reductase 6,7-dihydropteridine reductase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.34 1.5.1.34] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/6,7-dihydropteridine_reductase 6,7-dihydropteridine reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.34 1.5.1.34] </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=3bm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm1 OCA], [~~http~~://pdbe.org/3bm1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3bm1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3bm1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3bm1 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=3bm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm1 OCA], [https://pdbe.org/3bm1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bm1 RCSB], [https://www.ebi.ac.uk/pdbsum/3bm1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bm1 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bm/3bm1_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bm/3bm1_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 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 3bm1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3bm1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitroreductase\|Nitroreductase]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	[[Category: 6,7-dihydropteridine reductase]]		[[Category: 6,7-dihydropteridine reductase]]
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Choi, J W]]		[[Category: Choi, J W]]
	[[Category: Kim, J S]]		[[Category: Kim, J S]]

OCA at 08:06, 25 October 2017

OCA — Wed, 25 Oct 2017 08:06:11 GMT

←Older revision		Revision as of 08:06, 25 October 2017
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 3bm1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3bm1" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Nitroreductase\|Nitroreductase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:15, 11 August 2016

OCA — Thu, 11 Aug 2016 21:15:07 GMT

←Older revision		Revision as of 21:15, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of a minimal nitroreductase ydjA from Escherichia coli K12 with and without FMN cofactor==		==Crystal structure of a minimal nitroreductase ydjA from Escherichia coli K12 with and without FMN cofactor==
	<StructureSection load='3bm1' size='340' side='right' caption='[[3bm1]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3bm1' size='340' side='right' caption='[[3bm1]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bm1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia coli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BM1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bm1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BM1 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></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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bm2\|3bm2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bm2\|3bm2]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ydjA ([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">ydjA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6,7-dihydropteridine_reductase 6,7-dihydropteridine reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.34 1.5.1.34] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6,7-dihydropteridine_reductase 6,7-dihydropteridine reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.34 1.5.1.34] </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=3bm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bm1 RCSB], [http://www.ebi.ac.uk/pdbsum/3bm1 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=3bm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm1 OCA], [http://pdbe.org/3bm1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bm1 RCSB], [http://www.ebi.ac.uk/pdbsum/3bm1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3bm1 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 17:		Line 18:
	<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=3bm1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 28:
	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 3bm1" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: 6,7-dihydropteridine reductase]]		[[Category: 6,7-dihydropteridine reductase]]
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: Ecoli]]
	[[Category: Choi, J W]]		[[Category: Choi, J W]]
	[[Category: Kim, J S]]		[[Category: Kim, J S]]

OCA at 11:44, 20 January 2015

OCA — Tue, 20 Jan 2015 11:44:53 GMT

←Older revision		Revision as of 11:44, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3bm1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BM1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3bm1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BM1 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene><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></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bm2\|3bm2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bm2\|3bm2]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ydjA ([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">ydjA ([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>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6,7-dihydropteridine_reductase 6,7-dihydropteridine reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.34 1.5.1.34] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6,7-dihydropteridine_reductase 6,7-dihydropteridine reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.34 1.5.1.34] </span></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=3bm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bm1 RCSB], [http://www.ebi.ac.uk/pdbsum/3bm1 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=3bm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bm1 RCSB], [http://www.ebi.ac.uk/pdbsum/3bm1 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: 6,7-dihydropteridine reductase]]		[[Category: 6,7-dihydropteridine reductase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Choi, J W.]]	+	[[Category: Choi, J W]]
-	[[Category: Kim, J S.]]	+	[[Category: Kim, J S]]
	[[Category: Nitroreductase]]		[[Category: Nitroreductase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Ydja]]		[[Category: Ydja]]

OCA at 10:22, 29 September 2014

OCA — Mon, 29 Sep 2014 10:22:11 GMT

←Older revision		Revision as of 10:22, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3bm1.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of a minimal nitroreductase ydjA from Escherichia coli K12 with and without FMN cofactor==
		+	<StructureSection load='3bm1' size='340' side='right' caption='[[3bm1]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3bm1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BM1 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bm2\|3bm2]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ydjA ([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>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6,7-dihydropteridine_reductase 6,7-dihydropteridine reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.34 1.5.1.34] </span></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=3bm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bm1 RCSB], [http://www.ebi.ac.uk/pdbsum/3bm1 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/bm/3bm1_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 ==
		+	Nitroreductases (NTR) are enzymes that reduce hazardous nitroaromatic compounds and are of special interest due to their potential use in bioremediation and their activation of prodrugs in directed anticancer therapies. We elucidated the crystal structures of ydjA from Escherichia coli (Ec_ydjA), one of the smallest NTRs, in its flavin mononucleotide (FMN)-bound and cofactor-free forms. The alpha+beta mixed monomeric Ec_ydjA forms a homodimeric structure through the interactions of the long central helices and the extended regions at both termini. Two FMN molecules are bound at the dimeric interface. The absence of the 30 internal amino acids in Ec_ydjA, which forms two helices and restricts the cofactor and substrate binding in other NTR family members, creates a wider and more flexible active site. Unlike the bent FMN ring structures present in most NTR complexes currently known, the flavin system in the Ec_ydjA structure maintains a flat ring conformation, which is sandwiched between a Trp and a His residue from each monomer. The analysis of our Ec_ydjA structure explains its specificity for larger substrates and provides structural information for the rational design of novel prodrugs with the ability to reduce nitrogen-containing hazardous molecules.

-	~~{{STRUCTURE_3bm1\| PDB=3bm1 \| SCENE= }}~~	+	Crystal structure of a minimal nitroreductase, ydjA, from Escherichia coli K12 with and without FMN cofactor.,Choi JW, Lee J, Nishi K, Kim YS, Jung CH, Kim JS J Mol Biol. 2008 Mar 14;377(1):258-67. Epub 2008 Jan 11. PMID:18241886<ref>PMID:18241886</ref>

-	~~===Crystal structure~~ of ~~a minimal nitroreductase ydjA from Escherichia coli K12 with and without FMN cofactor===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18241886}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3bm1]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3BM1 OCA].~~	+

	==See Also==		==See Also==
	*[[Nitroreductase\|Nitroreductase]]		*[[Nitroreductase\|Nitroreductase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018241886<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: 6,7-dihydropteridine reductase]]		[[Category: 6,7-dihydropteridine reductase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA at 18:06, 20 October 2012

OCA — Sat, 20 Oct 2012 18:06:04 GMT

←Older revision		Revision as of 18:06, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3bm1]] is a 2 chain structure ~~of [[Nitroreductase]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM1 OCA].	+	[[3bm1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM1 OCA].

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

OCA: Protected "3bm1" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 03:01:14 GMT

Protected "3bm1" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:01, 27 July 2012

OCA at 03:01, 27 July 2012

OCA — Fri, 27 Jul 2012 03:01:13 GMT

←Older revision		Revision as of 03:01, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3bm1.png\|left\|200px]]		[[Image:3bm1.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3bm1", 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_3bm1\| PDB=3bm1 \| SCENE= }}		{{STRUCTURE_3bm1\| PDB=3bm1 \| SCENE= }}

	===Crystal structure of a minimal nitroreductase ydjA from Escherichia coli K12 with and without FMN cofactor===		===Crystal structure of a minimal nitroreductase ydjA from Escherichia coli K12 with and without FMN cofactor===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18241886}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18241886 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18241886}}		{{ABSTRACT_PUBMED_18241886}}

	==About this Structure==		==About this Structure==
-	~~3BM1~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM1 OCA].	+	[[3bm1]] is a 2 chain structure of [[Nitroreductase]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM1 OCA].
		+
		+	==See Also==
		+	*[[Nitroreductase\|Nitroreductase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18241886~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018241886</ref><references group="xtra"/>
	[[Category: 6,7-dihydropteridine reductase]]		[[Category: 6,7-dihydropteridine reductase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
Line 31:		Line 22:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Ydja]]		[[Category: Ydja]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 19:41:07 2009''

OCA at 17:41, 17 February 2009

OCA — Tue, 17 Feb 2009 17:41:07 GMT

←Older revision		Revision as of 17:41, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3BM1 is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM1 OCA].	+	3BM1 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM1 OCA].

	==Reference==		==Reference==
-	Crystal structure of a minimal nitroreductase, ydjA, from Escherichia coli K12 with and without FMN cofactor., Choi JW, Lee J, Nishi K, Kim YS, Jung CH, Kim JS, J Mol Biol. 2008 Mar 14;377(1):258-67. Epub 2008 Jan 11. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18241886 18241886]~~	+	<ref group="xtra">PMID:18241886</ref><references group="xtra"/>
	[[Category: 6,7-dihydropteridine reductase]]		[[Category: 6,7-dihydropteridine reductase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Choi, J W.]]		[[Category: Choi, J W.]]
	[[Category: Kim, J S.]]		[[Category: Kim, J S.]]
Line 33:		Line 32:
	[[Category: Ydja]]		[[Category: Ydja]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 03~~:33:~~36 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 19:41:07 2009''