3lxf - Revision history

OCA at 07:34, 9 January 2019

OCA — Wed, 09 Jan 2019 07:34:59 GMT

←Older revision		Revision as of 07:34, 9 January 2019
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lx/3lxf_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lx/3lxf_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>

OCA at 18:20, 11 August 2016

OCA — Thu, 11 Aug 2016 18:20:27 GMT

←Older revision		Revision as of 18:20, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of [2Fe-2S] Ferredoxin Arx from Novosphingobium aromaticivorans==		==Crystal Structure of [2Fe-2S] Ferredoxin Arx from Novosphingobium aromaticivorans==
	<StructureSection load='3lxf' size='340' side='right' caption='[[3lxf]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3lxf' size='340' side='right' caption='[[3lxf]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3lxd\|3lxd]], [[3lxh\|3lxh]], [[3lxi\|3lxi]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3lxd\|3lxd]], [[3lxh\|3lxh]], [[3lxi\|3lxi]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Saro_1477 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=279238 NOVAD])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Saro_1477 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=279238 NOVAD])</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=3lxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lxf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lxf RCSB], [http://www.ebi.ac.uk/pdbsum/3lxf 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=3lxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lxf OCA], [http://pdbe.org/3lxf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lxf RCSB], [http://www.ebi.ac.uk/pdbsum/3lxf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lxf ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 17:
	<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=3lxf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		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 3lxf" style="background-color:#fffaf0;"></div>

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

OCA at 08:29, 20 January 2015

OCA — Tue, 20 Jan 2015 08:29:30 GMT

←Older revision		Revision as of 08:29, 20 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_3lxf\| PDB=3lxf \| SCENE= }}~~	+	==Crystal Structure of [2Fe-2S] Ferredoxin Arx from Novosphingobium aromaticivorans==
-	===Crystal Structure of [2Fe-2S] Ferredoxin Arx from Novosphingobium aromaticivorans===	+	<StructureSection load='3lxf' size='340' side='right' caption='[[3lxf]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~{{ABSTRACT_PUBMED_20576606}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3lxf]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Novad Novad]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LXF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LXF FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3lxd\|3lxd]], [[3lxh\|3lxh]], [[3lxi\|3lxi]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Saro_1477 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=279238 NOVAD])</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=3lxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lxf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lxf RCSB], [http://www.ebi.ac.uk/pdbsum/3lxf 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/lx/3lxf_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 ==
		+	Cytochrome P450 (CYP) enzymes of the CYP101 and CYP111 families from the oligotrophic bacterium Novosphingobium aromaticivorans DSM12444 are heme monooxygenases that receive electrons from NADH via Arx, a [2Fe-2S] ferredoxin, and ArR, a ferredoxin reductase. These systems show fast NADH turnovers (k(cat) = 39-91 s(-1)) that are efficiently coupled to product formation. The three-dimensional structures of ArR, Arx, and CYP101D1, which form a physiological class I P450 electron transfer chain, have been resolved by x-ray crystallography. The general structural features of these proteins are similar to their counterparts in other class I systems such as putidaredoxin reductase (PdR), putidaredoxin (Pdx), and CYP101A1 of the camphor hydroxylase system from Pseudomonas putida, and adrenodoxin (Adx) of the mitochondrial steroidogenic CYP11 and CYP24A1 systems. However, significant differences in the proposed protein-protein interaction surfaces of the ferredoxin reductase, ferredoxin, and P450 enzyme are found. There are regions of positive charge on the likely interaction face of ArR and CYP101D1 and a corresponding negatively charged area on the surface of Arx. The [2Fe-2S] cluster binding loop in Arx also has a neutral, hydrophobic patch on the surface. These surface characteristics are more in common with those of Adx than Pdx. The observed structural features are consistent with the ionic strength dependence of the activity.

-	~~==About this Structure==~~	+	Molecular characterization of a class I P450 electron transfer system from Novosphingobium aromaticivorans DSM12444.,Yang W, Bell SG, Wang H, Zhou W, Hoskins N, Dale A, Bartlam M, Wong LL, Rao Z J Biol Chem. 2010 Aug 27;285(35):27372-84. Epub 2010 Jun 24. PMID:20576606<ref>PMID:20576606</ref>
-	~~[[3lxf]] is~~ a ~~5 chain structure with sequence~~ from ~~[http~~:~~//en~~.~~wikipedia~~.~~org/wiki/Novad Novad]. Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3LXF OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Ferredoxin\|Ferredoxin]]		*[[Ferredoxin\|Ferredoxin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:020576606</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Novad]]		[[Category: Novad]]
-	[[Category: Bartlam, M.]]	+	[[Category: Bartlam, M]]
-	[[Category: Bell, S G.]]	+	[[Category: Bell, S G]]
-	[[Category: Rao, Z.]]	+	[[Category: Rao, Z]]
-	[[Category: Wang, H.]]	+	[[Category: Wang, H]]
-	[[Category: Wong, L L.]]	+	[[Category: Wong, L L]]
-	[[Category: Yang, W.]]	+	[[Category: Yang, W]]
	[[Category: Iron]]		[[Category: Iron]]
	[[Category: Iron-sulfur]]		[[Category: Iron-sulfur]]
	[[Category: Metal binding protein]]		[[Category: Metal binding protein]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]

OCA at 04:06, 13 February 2014

OCA — Thu, 13 Feb 2014 04:06:59 GMT

←Older revision		Revision as of 04:06, 13 February 2014
Line 1:		Line 1:
-	[[Image:3lxf.png\|left\|200px]]
-
	{{STRUCTURE_3lxf\| PDB=3lxf \| SCENE= }}		{{STRUCTURE_3lxf\| PDB=3lxf \| SCENE= }}
-
	===Crystal Structure of [2Fe-2S] Ferredoxin Arx from Novosphingobium aromaticivorans===		===Crystal Structure of [2Fe-2S] Ferredoxin Arx from Novosphingobium aromaticivorans===
-
	{{ABSTRACT_PUBMED_20576606}}		{{ABSTRACT_PUBMED_20576606}}

	==About this Structure==		==About this Structure==
-	[[3lxf]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Novosphingobium_aromaticivorans Novosphingobium aromaticivorans~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LXF OCA].	+	[[3lxf]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Novad Novad]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LXF OCA].

	==See Also==		==See Also==
Line 14:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:020576606</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020576606</ref><references group="xtra"/><references/>
-	[[Category: ~~Novosphingobium aromaticivorans~~]]	+	[[Category: Novad]]
	[[Category: Bartlam, M.]]		[[Category: Bartlam, M.]]
	[[Category: Bell, S G.]]		[[Category: Bell, S G.]]

OCA at 12:59, 20 October 2012

OCA — Sat, 20 Oct 2012 12:59:30 GMT

←Older revision		Revision as of 12:59, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3lxf]] is a 5 chain structure ~~of [[Ferredoxin]]~~ with sequence from [http://en.wikipedia.org/wiki/Novosphingobium_aromaticivorans Novosphingobium aromaticivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LXF OCA].	+	[[3lxf]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Novosphingobium_aromaticivorans Novosphingobium aromaticivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LXF OCA].

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

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

OCA — Thu, 26 Jul 2012 10:33:24 GMT

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

←Older revision

Revision as of 10:33, 26 July 2012

OCA at 10:33, 26 July 2012

OCA — Thu, 26 Jul 2012 10:33:22 GMT

←Older revision		Revision as of 10:33, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3lxf.png\|left\|200px]]		[[Image:3lxf.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3lxf", 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_3lxf\| PDB=3lxf \| SCENE= }}		{{STRUCTURE_3lxf\| PDB=3lxf \| SCENE= }}

	===Crystal Structure of [2Fe-2S] Ferredoxin Arx from Novosphingobium aromaticivorans===		===Crystal Structure of [2Fe-2S] Ferredoxin Arx from Novosphingobium aromaticivorans===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20576606}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20576606 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20576606}}		{{ABSTRACT_PUBMED_20576606}}

	==About this Structure==		==About this Structure==
-	~~3LXF~~ is a 5 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Novosphingobium_aromaticivorans Novosphingobium aromaticivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LXF OCA].	+	[[3lxf]] is a 5 chain structure of [[Ferredoxin]] with sequence from [http://en.wikipedia.org/wiki/Novosphingobium_aromaticivorans Novosphingobium aromaticivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LXF OCA].
		+
		+	==See Also==
		+	*[[Ferredoxin\|Ferredoxin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20576606~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020576606</ref><references group="xtra"/>
	[[Category: Novosphingobium aromaticivorans]]		[[Category: Novosphingobium aromaticivorans]]
	[[Category: Bartlam, M.]]		[[Category: Bartlam, M.]]
Line 35:		Line 26:
	[[Category: Metal binding protein]]		[[Category: Metal binding protein]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 7 08:16:58 2010''

OCA at 04:11, 7 July 2010

OCA — Wed, 07 Jul 2010 04:11:25 GMT

←Older revision		Revision as of 04:11, 7 July 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3lxf.~~jpg~~\|left\|200px]]	+	[[Image:3lxf.png\|left\|200px]]

	<!--		<!--
Line 12:		Line 12:
	===Crystal Structure of [2Fe-2S] Ferredoxin Arx from Novosphingobium aromaticivorans===		===Crystal Structure of [2Fe-2S] Ferredoxin Arx from Novosphingobium aromaticivorans===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20576606}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20576606 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20576606}}

	==About this Structure==		==About this Structure==
	3LXF is a 5 chains structure with sequences from [http://en.wikipedia.org/wiki/Novosphingobium_aromaticivorans Novosphingobium aromaticivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LXF OCA].		3LXF is a 5 chains structure with sequences from [http://en.wikipedia.org/wiki/Novosphingobium_aromaticivorans Novosphingobium aromaticivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LXF OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20576606</ref><references group="xtra"/>
	[[Category: Novosphingobium aromaticivorans]]		[[Category: Novosphingobium aromaticivorans]]
	[[Category: Bartlam, M.]]		[[Category: Bartlam, M.]]
Line 27:		Line 36:
	[[Category: Metal-binding]]		[[Category: Metal-binding]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jun 23~~ 08:50:17 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 7 08:16:58 2010''

OCA at 04:45, 23 June 2010

OCA — Wed, 23 Jun 2010 04:45:00 GMT

←Older revision		Revision as of 04:45, 23 June 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3lxf.jpg\|left\|200px]]

-	The ~~entry 3lxf~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3lxf", 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_3lxf\| PDB=3lxf \| SCENE= }}

-	~~Authors: Yang, W., Bell, S.G., Wang, H., Bartlam, M., Wong, L.L., Rao, Z.~~	+	===Crystal Structure of [2Fe-2S] Ferredoxin Arx from Novosphingobium aromaticivorans===

-	Description: Crystal Structure of [2Fe-2S] Ferredoxin Arx from Novosphingobium aromaticivorans

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~May 5 11~~:37:13 2010''	+	==About this Structure==
		+	3LXF is a 5 chains structure with sequences from [http://en.wikipedia.org/wiki/Novosphingobium_aromaticivorans Novosphingobium aromaticivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LXF OCA].
		+	[[Category: Novosphingobium aromaticivorans]]
		+	[[Category: Bartlam, M.]]
		+	[[Category: Bell, S G.]]
		+	[[Category: Rao, Z.]]
		+	[[Category: Wang, H.]]
		+	[[Category: Wong, L L.]]
		+	[[Category: Yang, W.]]
		+	[[Category: Iron]]
		+	[[Category: Iron-sulfur]]
		+	[[Category: Metal binding protein]]
		+	[[Category: Metal-binding]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 23 08:50:17 2010''

OCA at 08:37, 5 May 2010

OCA — Wed, 05 May 2010 08:37:13 GMT

←Older revision		Revision as of 08:37, 5 May 2010
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3lxf is ON HOLD	+	The entry 3lxf is ON HOLD until Paper Publication

	Authors: Yang, W., Bell, S.G., Wang, H., Bartlam, M., Wong, L.L., Rao, Z.		Authors: Yang, W., Bell, S.G., Wang, H., Bartlam, M., Wong, L.L., Rao, Z.
Line 7:		Line 7:
	Description: Crystal Structure of [2Fe-2S] Ferredoxin Arx from Novosphingobium aromaticivorans		Description: Crystal Structure of [2Fe-2S] Ferredoxin Arx from Novosphingobium aromaticivorans

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Mar 10 13~~:16:14 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 5 11:37:13 2010''