1m2b - Revision history

OCA at 07:38, 14 February 2024

OCA — Wed, 14 Feb 2024 07:38:55 GMT

←Older revision		Revision as of 07:38, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1m2b' size='340' side='right'caption='[[1m2b]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1m2b' size='340' side='right'caption='[[1m2b]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m2b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex~~ aeolicus~~" huber and stetter 2001~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M2B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m2b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M2B FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</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]] 1.25Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[1f37\|1f37]], [[1m2a\|1m2a]], [[1m2d\|1m2d]]~~<~~/div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]<~~/b></td>~~<td class="sblockDat">Fdx4 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])~~</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=1m2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2b OCA], [https://pdbe.org/1m2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m2b RCSB], [https://www.ebi.ac.uk/pdbsum/1m2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2b 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=1m2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2b OCA], [https://pdbe.org/1m2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m2b RCSB], [https://www.ebi.ac.uk/pdbsum/1m2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/FER2_AQUAE FER2_AQUAE]] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.	+	[https://www.uniprot.org/uniprot/FER2_AQUAE FER2_AQUAE] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</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=1m2b 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=1m2b ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The [2Fe-2S] ferredoxin (Fd4) from Aquifex aeolicus adopts a thioredoxin-like polypeptide fold that is distinct from other [2Fe-2S] ferredoxins. Crystal structures of the Cys-55 --> Ser (C55S) and Cys-59 --> Ser (C59S) variants of this protein have been determined to 1.25 A and 1.05 A resolution, respectively, whereas the resolution of the wild type (WT) has been extended to 1.5 A. The improved WT structure provides a detailed description of the [2Fe-2S] cluster, including two features that have not been noted previously in any [2Fe-2S] cluster-containing protein, namely, pronounced distortions in the cysteine coordination to the cluster and a Calpha-H-Sgamma hydrogen bond between cluster ligands Cys-55 and Cys-9. These features may contribute to the unusual electronic and magnetic properties of the [2Fe-2S] clusters in WT and variants of this ferredoxin. The structures of the two variants of Fd4, in which single cysteine ligands to the [2Fe-2S] cluster are replaced by serine, establish the metric details of serine-ligated Fe-S active sites with unprecedented accuracy. Both the cluster and its surrounding protein matrix change in subtle ways to accommodate this ligand substitution, particularly in terms of distortions of the Fe(2)S(2) inorganic core from planarity and displacements of the polypeptide chain. These high resolution structures illustrate how the interactions between polypeptide chains and Fe-S active sites reflect combinations of flexibility and rigidity on the part of both partners; these themes are also evident in more complex systems, as exemplified by changes associated with serine ligation of the nitrogenase P cluster.
-
-	High resolution crystal structures of the wild type and Cys-55-->Ser and Cys-59-->Ser variants of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus.,Yeh AP, Ambroggio XI, Andrade SL, Einsle O, Chatelet C, Meyer J, Rees DC J Biol Chem. 2002 Sep 13;277(37):34499-507. Epub 2002 Jun 27. PMID:12089152<ref>PMID:12089152</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1m2b" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ferredoxin 3D structures\|Ferredoxin 3D structures]]		*[[Ferredoxin 3D structures\|Ferredoxin 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Aquifex aeolicus ~~huber and stetter 2001~~]]	+	[[Category: Aquifex aeolicus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ambroggio~~, X I~~]]	+	[[Category: Ambroggio XI]]
-	[[Category: Andrade~~, S L.A~~]]	+	[[Category: Andrade SLA]]
-	[[Category: Chatelet, C]]	+	[[Category: Chatelet C]]
-	[[Category: Einsle, O]]	+	[[Category: Einsle O]]
-	[[Category: Meyer, J]]	+	[[Category: Meyer J]]
-	[[Category: Rees~~, D C~~]]	+	[[Category: Rees DC]]
-	[[Category: Yeh~~, A P]]~~	+	[[Category: Yeh AP]]
-	~~[[Category: Cys55ser variant]]~~	+
-	~~[[Category: Electron transport]]~~	+
-	~~[[Category: Ferredoxin]]~~	+
-	~~[[Category: Thioredoxin-like fold~~]]	+

OCA at 14:52, 27 October 2021

OCA — Wed, 27 Oct 2021 14:52:17 GMT

←Older revision		Revision as of 14:52, 27 October 2021
Line 3:		Line 3:
	<StructureSection load='1m2b' size='340' side='right'caption='[[1m2b]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1m2b' size='340' side='right'caption='[[1m2b]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m2b]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1M2B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m2b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M2B FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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"><div style='overflow: auto; max-height: 3em;'>[[1f37\|1f37]], [[1m2a\|1m2a]], [[1m2d\|1m2d]]</div></td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1f37\|1f37]], [[1m2a\|1m2a]], [[1m2d\|1m2d]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Fdx4 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Fdx4 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1m2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2b OCA], [~~http~~://pdbe.org/1m2b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1m2b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1m2b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2b 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=1m2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2b OCA], [https://pdbe.org/1m2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m2b RCSB], [https://www.ebi.ac.uk/pdbsum/1m2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/FER2_AQUAE FER2_AQUAE]] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.	+	[[https://www.uniprot.org/uniprot/FER2_AQUAE FER2_AQUAE]] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:32, 2 December 2020

OCA — Wed, 02 Dec 2020 08:32:17 GMT

←Older revision		Revision as of 08:32, 2 December 2020
Line 1:		Line 1:

	==Crystal structure at 1.25 Angstroms resolution of the Cys55Ser variant of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus==		==Crystal structure at 1.25 Angstroms resolution of the Cys55Ser variant of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus==
-	<StructureSection load='1m2b' size='340' side='right' caption='[[1m2b]], [[Resolution\|resolution]] 1.25Å' scene=''>	+	<StructureSection load='1m2b' size='340' side='right'caption='[[1m2b]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m2b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2B OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1M2B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m2b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2B OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1M2B 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>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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">[[1f37\|1f37]], [[1m2a\|1m2a]], [[1m2d\|1m2d]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1f37\|1f37]], [[1m2a\|1m2a]], [[1m2d\|1m2d]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Fdx4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Fdx4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</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=1m2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2b OCA], [http://pdbe.org/1m2b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m2b RCSB], [http://www.ebi.ac.uk/pdbsum/1m2b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2b ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1m2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2b OCA], [http://pdbe.org/1m2b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m2b RCSB], [http://www.ebi.ac.uk/pdbsum/1m2b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1m2b" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1m2b" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ferredoxin 3D structures\|Ferredoxin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Aquifex aeolicus huber and stetter 2001]]		[[Category: Aquifex aeolicus huber and stetter 2001]]
		+	[[Category: Large Structures]]
	[[Category: Ambroggio, X I]]		[[Category: Ambroggio, X I]]
	[[Category: Andrade, S L.A]]		[[Category: Andrade, S L.A]]

OCA at 07:44, 31 January 2018

OCA — Wed, 31 Jan 2018 07:44:33 GMT

←Older revision		Revision as of 07:44, 31 January 2018
Line 1:		Line 1:
		+
	==Crystal structure at 1.25 Angstroms resolution of the Cys55Ser variant of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus==		==Crystal structure at 1.25 Angstroms resolution of the Cys55Ser variant of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus==
	<StructureSection load='1m2b' size='340' side='right' caption='[[1m2b]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1m2b' size='340' side='right' caption='[[1m2b]], [[Resolution\|resolution]] 1.25Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f37\|1f37]], [[1m2a\|1m2a]], [[1m2d\|1m2d]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f37\|1f37]], [[1m2a\|1m2a]], [[1m2d\|1m2d]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Fdx4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Fdx4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</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=1m2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2b OCA], [http://pdbe.org/1m2b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m2b RCSB], [http://www.ebi.ac.uk/pdbsum/1m2b 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=1m2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2b OCA], [http://pdbe.org/1m2b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m2b RCSB], [http://www.ebi.ac.uk/pdbsum/1m2b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m2/1m2b_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m2/1m2b_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 30:
	</div>		</div>
	<div class="pdbe-citations 1m2b" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1m2b" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Ferredoxin\|Ferredoxin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:18, 10 February 2016

OCA — Wed, 10 Feb 2016 04:18:01 GMT

←Older revision		Revision as of 04:18, 10 February 2016
Line 18:		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=1m2b ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:18, 11 September 2015

OCA — Fri, 11 Sep 2015 05:18:35 GMT

←Older revision		Revision as of 05:18, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1m2b' size='340' side='right' caption='[[1m2b]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1m2b' size='340' side='right' caption='[[1m2b]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m2b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Aquifex_aeolicus Aquifex~~ aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M2B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m2b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M2B 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>		</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">[[1f37\|1f37]], [[1m2a\|1m2a]], [[1m2d\|1m2d]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f37\|1f37]], [[1m2a\|1m2a]], [[1m2d\|1m2d]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Fdx4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Fdx4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</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=1m2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m2b RCSB], [http://www.ebi.ac.uk/pdbsum/1m2b 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=1m2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2b OCA], [http://pdbe.org/1m2b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m2b RCSB], [http://www.ebi.ac.uk/pdbsum/1m2b PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		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 1m2b" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Aquifex aeolicus]]	+	[[Category: Aquifex aeolicus huber and stetter 2001]]
	[[Category: Ambroggio, X I]]		[[Category: Ambroggio, X I]]
	[[Category: Andrade, S L.A]]		[[Category: Andrade, S L.A]]

OCA at 11:44, 25 December 2014

OCA — Thu, 25 Dec 2014 11:44:43 GMT

←Older revision		Revision as of 11:44, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1m2b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M2B FirstGlance]. <br>		<table><tr><td colspan='2'>[[1m2b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M2B FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene><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><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f37\|1f37]], [[1m2a\|1m2a]], [[1m2d\|1m2d]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f37\|1f37]], [[1m2a\|1m2a]], [[1m2d\|1m2d]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Fdx4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Fdx4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])</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=1m2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m2b RCSB], [http://www.ebi.ac.uk/pdbsum/1m2b 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=1m2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m2b RCSB], [http://www.ebi.ac.uk/pdbsum/1m2b PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FER2_AQUAE FER2_AQUAE]] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
-	[[Category: Ambroggio, X I.]]	+	[[Category: Ambroggio, X I]]
-	[[Category: Andrade, S L.A.]]	+	[[Category: Andrade, S L.A]]
-	[[Category: Chatelet, C.]]	+	[[Category: Chatelet, C]]
-	[[Category: Einsle, O.]]	+	[[Category: Einsle, O]]
-	[[Category: Meyer, J.]]	+	[[Category: Meyer, J]]
-	[[Category: Rees, D C.]]	+	[[Category: Rees, D C]]
-	[[Category: Yeh, A P.]]	+	[[Category: Yeh, A P]]
	[[Category: Cys55ser variant]]		[[Category: Cys55ser variant]]
	[[Category: Electron transport]]		[[Category: Electron transport]]
	[[Category: Ferredoxin]]		[[Category: Ferredoxin]]
	[[Category: Thioredoxin-like fold]]		[[Category: Thioredoxin-like fold]]

OCA at 13:40, 28 September 2014

OCA — Sun, 28 Sep 2014 13:40:50 GMT

←Older revision		Revision as of 13:40, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1m2b.~~png~~\|~~left~~\|200px]]	+	==Crystal structure at 1.25 Angstroms resolution of the Cys55Ser variant of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus==
		+	<StructureSection load='1m2b' size='340' side='right' caption='[[1m2b]], [[Resolution\|resolution]] 1.25Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1m2b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M2B FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f37\|1f37]], [[1m2a\|1m2a]], [[1m2d\|1m2d]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Fdx4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])</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=1m2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m2b RCSB], [http://www.ebi.ac.uk/pdbsum/1m2b 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/m2/1m2b_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 ==
		+	The [2Fe-2S] ferredoxin (Fd4) from Aquifex aeolicus adopts a thioredoxin-like polypeptide fold that is distinct from other [2Fe-2S] ferredoxins. Crystal structures of the Cys-55 --> Ser (C55S) and Cys-59 --> Ser (C59S) variants of this protein have been determined to 1.25 A and 1.05 A resolution, respectively, whereas the resolution of the wild type (WT) has been extended to 1.5 A. The improved WT structure provides a detailed description of the [2Fe-2S] cluster, including two features that have not been noted previously in any [2Fe-2S] cluster-containing protein, namely, pronounced distortions in the cysteine coordination to the cluster and a Calpha-H-Sgamma hydrogen bond between cluster ligands Cys-55 and Cys-9. These features may contribute to the unusual electronic and magnetic properties of the [2Fe-2S] clusters in WT and variants of this ferredoxin. The structures of the two variants of Fd4, in which single cysteine ligands to the [2Fe-2S] cluster are replaced by serine, establish the metric details of serine-ligated Fe-S active sites with unprecedented accuracy. Both the cluster and its surrounding protein matrix change in subtle ways to accommodate this ligand substitution, particularly in terms of distortions of the Fe(2)S(2) inorganic core from planarity and displacements of the polypeptide chain. These high resolution structures illustrate how the interactions between polypeptide chains and Fe-S active sites reflect combinations of flexibility and rigidity on the part of both partners; these themes are also evident in more complex systems, as exemplified by changes associated with serine ligation of the nitrogenase P cluster.

-	~~{{STRUCTURE_1m2b\| PDB=1m2b \| SCENE= }}~~	+	High resolution crystal structures of the wild type and Cys-55-->Ser and Cys-59-->Ser variants of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus.,Yeh AP, Ambroggio XI, Andrade SL, Einsle O, Chatelet C, Meyer J, Rees DC J Biol Chem. 2002 Sep 13;277(37):34499-507. Epub 2002 Jun 27. PMID:12089152<ref>PMID:12089152</ref>

-	~~===Crystal structure at 1.25 Angstroms resolution~~ of the ~~Cys55Ser variant of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12089152}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1m2b]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Aquifex_aeolicus Aquifex aeolicus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1M2B OCA].~~	+

	==See Also==		==See Also==
	*[[Ferredoxin\|Ferredoxin]]		*[[Ferredoxin\|Ferredoxin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012089152<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
	[[Category: Ambroggio, X I.]]		[[Category: Ambroggio, X I.]]

OCA at 16:18, 20 October 2012

OCA — Sat, 20 Oct 2012 16:18:16 GMT

←Older revision		Revision as of 16:18, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1m2b]] is a 2 chain structure ~~of [[Ferredoxin]]~~ with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2B OCA].	+	[[1m2b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2B OCA].

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

OCA at 21:14, 26 July 2012

OCA — Thu, 26 Jul 2012 21:14:13 GMT

←Older revision		Revision as of 21:14, 26 July 2012
Line 1:		Line 1:
	[[Image:1m2b.png\|left\|200px]]		[[Image:1m2b.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1m2b", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
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-	or leave the SCENE parameter empty for the default display.
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	{{STRUCTURE_1m2b\| PDB=1m2b \| SCENE= }}		{{STRUCTURE_1m2b\| PDB=1m2b \| SCENE= }}

	===Crystal structure at 1.25 Angstroms resolution of the Cys55Ser variant of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus===		===Crystal structure at 1.25 Angstroms resolution of the Cys55Ser variant of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12089152}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12089152 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_12089152}}		{{ABSTRACT_PUBMED_12089152}}

Line 22:		Line 11:

	==See Also==		==See Also==
-	*[[Ferredoxin]]	+	*[[Ferredoxin\|Ferredoxin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12089152~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012089152</ref><references group="xtra"/>
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
	[[Category: Ambroggio, X I.]]		[[Category: Ambroggio, X I.]]