3e1m - Revision history

OCA at 09:44, 21 February 2024

2024-02-21T09:44:01Z

←Older revision		Revision as of 09:44, 21 February 2024
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	<StructureSection load='3e1m' size='340' side='right'caption='[[3e1m]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3e1m' size='340' side='right'caption='[[3e1m]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3e1m]] is a 12 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=3E1M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E1M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3e1m]] is a 12 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=3E1M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E1M FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>~~, ~~<scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.7Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3e1j\|3e1j]], [[3e1l\|3e1l]], [[3e1n\|3e1n]], [[3e1o\|3e1o]], [[3e1p\|3e1p]], [[3e1q\|3e1q]]~~</~~div~~><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">BFR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])~~</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=3e1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e1m OCA], [https://pdbe.org/3e1m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e1m RCSB], [https://www.ebi.ac.uk/pdbsum/3e1m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e1m 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=3e1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e1m OCA], [https://pdbe.org/3e1m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e1m RCSB], [https://www.ebi.ac.uk/pdbsum/3e1m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e1m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/BFR_ECOLI BFR_ECOLI]] Iron-storage protein, whose ferroxidase center binds Fe(2+) ions, oxidizes them by dioxygen to Fe(3+), and participates in the subsequent Fe(3+) oxide mineral core formation within the central cavity of the protein complex. The mineralized iron core can contain as many as 2700 iron atoms/24-meric molecule.<ref>PMID:10769150</ref> <ref>PMID:14636073</ref>	+	[https://www.uniprot.org/uniprot/BFR_ECOLI BFR_ECOLI] Iron-storage protein, whose ferroxidase center binds Fe(2+) ions, oxidizes them by dioxygen to Fe(3+), and participates in the subsequent Fe(3+) oxide mineral core formation within the central cavity of the protein complex. The mineralized iron core can contain as many as 2700 iron atoms/24-meric molecule.<ref>PMID:10769150</ref> <ref>PMID:14636073</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=3e1m 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=3e1m ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Ferritin proteins function to detoxify, solubilize and store cellular iron by directing the synthesis of a ferric oxyhydroxide mineral solubilized within the protein's central cavity. Here, through the application of X-ray crystallographic and kinetic methods, we report significant new insight into the mechanism of mineralization in a bacterioferritin (BFR). The structures of nonheme iron-free and di-Fe(2+) forms of BFR showed that the intrasubunit catalytic center, known as the ferroxidase center, is preformed, ready to accept Fe(2+) ions with little or no reorganization. Oxidation of the di-Fe(2+) center resulted in a di-Fe(3+) center, with bridging electron density consistent with a mu-oxo or hydro bridged species. The mu-oxo bridged di-Fe(3+) center appears to be stable, and there is no evidence that Fe(3+)species are transferred into the core from the ferroxidase center. Most significantly, the data also revealed a novel Fe(2+) binding site on the inner surface of the protein, lying approximately 10 A directly below the ferroxidase center, coordinated by only two residues, His46 and Asp50. Kinetic studies of variants containing substitutions of these residues showed that the site is functionally important. In combination, the data support a model in which the ferroxidase center functions as a true catalytic cofactor, rather than as a pore for the transfer of iron into the central cavity, as found for eukaryotic ferritins. The inner surface iron site appears to be important for the transfer of electrons, derived from Fe(2+) oxidation in the cavity, to the ferroxidase center. Bacterioferritin may represent an evolutionary link between ferritins and class II di-iron proteins not involved in iron metabolism.
-
-	Structural basis for iron mineralization by bacterioferritin.,Crow A, Lawson TL, Lewin A, Moore GR, Le Brun NE J Am Chem Soc. 2009 May 20;131(19):6808-13. PMID:19391621<ref>PMID:19391621</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3e1m" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Brun, N Le]]~~	+	[[Category: Crow A]]
-	[[Category: Crow, A]]	+	[[Category: Lawson T]]
-	[[Category: Lawson, T]]	+	[[Category: Le Brun N]]
-	[[Category: ~~Lewin, A~~]]	+	[[Category: Lewin A]]
-	[[Category: ~~Moore, G R~~]]	+	[[Category: Moore GR]]
-	[[Category: ~~Bacterioferritin. rhombic dodecahedral superstructure]]~~	+
-	~~[[Category: Heme]]~~	+
-	~~[[Category: Iron]]~~	+
-	~~[[Category: Iron storage]]~~	+
-	~~[[Category: Metal binding protein]]~~	+
-	~~[[Category: Metal-binding~~]]	+

OCA at 08:13, 9 February 2022

2022-02-09T08:13:06Z

←Older revision		Revision as of 08:13, 9 February 2022
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	==Crystal structure of E. coli Bacterioferritin (BFR) obtained after soaking APO-BFR crystals for 2.5 minutes in FE2+ (2.5M FE(II)-BFR)==		==Crystal structure of E. coli Bacterioferritin (BFR) obtained after soaking APO-BFR crystals for 2.5 minutes in FE2+ (2.5M FE(II)-BFR)==
-	<StructureSection load='3e1m' size='340' side='right' caption='[[3e1m]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='3e1m' size='340' side='right'caption='[[3e1m]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3e1m]] is a 12 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=3E1M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3E1M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3e1m]] is a 12 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=3E1M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E1M FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e1j\|3e1j]], [[3e1l\|3e1l]], [[3e1n\|3e1n]], [[3e1o\|3e1o]], [[3e1p\|3e1p]], [[3e1q\|3e1q]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3e1j\|3e1j]], [[3e1l\|3e1l]], [[3e1n\|3e1n]], [[3e1o\|3e1o]], [[3e1p\|3e1p]], [[3e1q\|3e1q]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BFR ([~~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">BFR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3e1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e1m OCA], [~~http~~://pdbe.org/3e1m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3e1m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3e1m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3e1m 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=3e1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e1m OCA], [https://pdbe.org/3e1m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e1m RCSB], [https://www.ebi.ac.uk/pdbsum/3e1m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e1m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/BFR_ECOLI BFR_ECOLI]] Iron-storage protein, whose ferroxidase center binds Fe(2+) ions, oxidizes them by dioxygen to Fe(3+), and participates in the subsequent Fe(3+) oxide mineral core formation within the central cavity of the protein complex. The mineralized iron core can contain as many as 2700 iron atoms/24-meric molecule.<ref>PMID:10769150</ref> <ref>PMID:14636073</ref>	+	[[https://www.uniprot.org/uniprot/BFR_ECOLI BFR_ECOLI]] Iron-storage protein, whose ferroxidase center binds Fe(2+) ions, oxidizes them by dioxygen to Fe(3+), and participates in the subsequent Fe(3+) oxide mineral core formation within the central cavity of the protein complex. The mineralized iron core can contain as many as 2700 iron atoms/24-meric molecule.<ref>PMID:10769150</ref> <ref>PMID:14636073</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
-	*[[Ferritin\|Ferritin]]	+	*[[Ferritin 3D structures\|Ferritin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Brun, N Le]]		[[Category: Brun, N Le]]
	[[Category: Crow, A]]		[[Category: Crow, A]]

OCA at 09:41, 14 November 2018

2018-11-14T09:41:31Z

←Older revision		Revision as of 09:41, 14 November 2018
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		+
	==Crystal structure of E. coli Bacterioferritin (BFR) obtained after soaking APO-BFR crystals for 2.5 minutes in FE2+ (2.5M FE(II)-BFR)==		==Crystal structure of E. coli Bacterioferritin (BFR) obtained after soaking APO-BFR crystals for 2.5 minutes in FE2+ (2.5M FE(II)-BFR)==
	<StructureSection load='3e1m' size='340' side='right' caption='[[3e1m]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3e1m' size='340' side='right' caption='[[3e1m]], [[Resolution\|resolution]] 2.70Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e1j\|3e1j]], [[3e1l\|3e1l]], [[3e1n\|3e1n]], [[3e1o\|3e1o]], [[3e1p\|3e1p]], [[3e1q\|3e1q]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e1j\|3e1j]], [[3e1l\|3e1l]], [[3e1n\|3e1n]], [[3e1o\|3e1o]], [[3e1p\|3e1p]], [[3e1q\|3e1q]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BFR ([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">BFR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3e1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e1m OCA], [http://pdbe.org/3e1m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e1m RCSB], [http://www.ebi.ac.uk/pdbsum/3e1m 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=3e1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e1m OCA], [http://pdbe.org/3e1m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e1m RCSB], [http://www.ebi.ac.uk/pdbsum/3e1m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3e1m 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/e1/3e1m_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e1/3e1m_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 11:46, 9 February 2016

2016-02-09T11:46:06Z

←Older revision		Revision as of 11:46, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3e1m' size='340' side='right' caption='[[3e1m]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3e1m' size='340' side='right' caption='[[3e1m]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3e1m]] is a 12 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=3E1M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E1M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3e1m]] is a 12 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=3E1M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E1M FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e1j\|3e1j]], [[3e1l\|3e1l]], [[3e1n\|3e1n]], [[3e1o\|3e1o]], [[3e1p\|3e1p]], [[3e1q\|3e1q]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e1j\|3e1j]], [[3e1l\|3e1l]], [[3e1n\|3e1n]], [[3e1o\|3e1o]], [[3e1p\|3e1p]], [[3e1q\|3e1q]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BFR ([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">BFR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3e1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e1m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e1m RCSB], [http://www.ebi.ac.uk/pdbsum/3e1m 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=3e1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e1m OCA], [http://pdbe.org/3e1m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e1m RCSB], [http://www.ebi.ac.uk/pdbsum/3e1m PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	<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=3e1m ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 3e1m" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: Ecoli]]
	[[Category: Brun, N Le]]		[[Category: Brun, N Le]]
	[[Category: Crow, A]]		[[Category: Crow, A]]

OCA at 06:35, 25 December 2014

2014-12-25T06:35:48Z

←Older revision		Revision as of 06:35, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3e1m]] is a 12 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=3E1M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E1M FirstGlance]. <br>		<table><tr><td colspan='2'>[[3e1m]] is a 12 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=3E1M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E1M FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e1j\|3e1j]], [[3e1l\|3e1l]], [[3e1n\|3e1n]], [[3e1o\|3e1o]], [[3e1p\|3e1p]], [[3e1q\|3e1q]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e1j\|3e1j]], [[3e1l\|3e1l]], [[3e1n\|3e1n]], [[3e1o\|3e1o]], [[3e1p\|3e1p]], [[3e1q\|3e1q]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BFR ([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">BFR ([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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3e1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e1m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e1m RCSB], [http://www.ebi.ac.uk/pdbsum/3e1m 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=3e1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e1m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e1m RCSB], [http://www.ebi.ac.uk/pdbsum/3e1m PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BFR_ECOLI BFR_ECOLI]] Iron-storage protein, whose ferroxidase center binds Fe(2+) ions, oxidizes them by dioxygen to Fe(3+), and participates in the subsequent Fe(3+) oxide mineral core formation within the central cavity of the protein complex. The mineralized iron core can contain as many as 2700 iron atoms/24-meric molecule.<ref>PMID:10769150</ref> <ref>PMID:14636073</ref>
	== 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: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Brun, N Le.]]	+	[[Category: Brun, N Le]]
-	[[Category: Crow, A.]]	+	[[Category: Crow, A]]
-	[[Category: Lawson, T.]]	+	[[Category: Lawson, T]]
-	[[Category: Lewin, A.]]	+	[[Category: Lewin, A]]
-	[[Category: Moore, G R.]]	+	[[Category: Moore, G R]]
-	[[Category: Bacterioferritin. rhombic dodecahedral superstructure.]]	+	[[Category: Bacterioferritin. rhombic dodecahedral superstructure]]
	[[Category: Heme]]		[[Category: Heme]]
	[[Category: Iron]]		[[Category: Iron]]

OCA at 13:15, 29 September 2014

2014-09-29T13:15:14Z

←Older revision		Revision as of 13:15, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3e1m.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of E. coli Bacterioferritin (BFR) obtained after soaking APO-BFR crystals for 2.5 minutes in FE2+ (2.5M FE(II)-BFR)==
		+	<StructureSection load='3e1m' size='340' side='right' caption='[[3e1m]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3e1m]] is a 12 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=3E1M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E1M FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e1j\|3e1j]], [[3e1l\|3e1l]], [[3e1n\|3e1n]], [[3e1o\|3e1o]], [[3e1p\|3e1p]], [[3e1q\|3e1q]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BFR ([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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3e1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e1m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e1m RCSB], [http://www.ebi.ac.uk/pdbsum/3e1m 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/e1/3e1m_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 ==
		+	Ferritin proteins function to detoxify, solubilize and store cellular iron by directing the synthesis of a ferric oxyhydroxide mineral solubilized within the protein's central cavity. Here, through the application of X-ray crystallographic and kinetic methods, we report significant new insight into the mechanism of mineralization in a bacterioferritin (BFR). The structures of nonheme iron-free and di-Fe(2+) forms of BFR showed that the intrasubunit catalytic center, known as the ferroxidase center, is preformed, ready to accept Fe(2+) ions with little or no reorganization. Oxidation of the di-Fe(2+) center resulted in a di-Fe(3+) center, with bridging electron density consistent with a mu-oxo or hydro bridged species. The mu-oxo bridged di-Fe(3+) center appears to be stable, and there is no evidence that Fe(3+)species are transferred into the core from the ferroxidase center. Most significantly, the data also revealed a novel Fe(2+) binding site on the inner surface of the protein, lying approximately 10 A directly below the ferroxidase center, coordinated by only two residues, His46 and Asp50. Kinetic studies of variants containing substitutions of these residues showed that the site is functionally important. In combination, the data support a model in which the ferroxidase center functions as a true catalytic cofactor, rather than as a pore for the transfer of iron into the central cavity, as found for eukaryotic ferritins. The inner surface iron site appears to be important for the transfer of electrons, derived from Fe(2+) oxidation in the cavity, to the ferroxidase center. Bacterioferritin may represent an evolutionary link between ferritins and class II di-iron proteins not involved in iron metabolism.

-	~~{{STRUCTURE_3e1m\| PDB=3e1m \| SCENE= }}~~	+	Structural basis for iron mineralization by bacterioferritin.,Crow A, Lawson TL, Lewin A, Moore GR, Le Brun NE J Am Chem Soc. 2009 May 20;131(19):6808-13. PMID:19391621<ref>PMID:19391621</ref>

-	~~===Crystal structure~~ of E. ~~coli Bacterioferritin (BFR) obtained after soaking APO-BFR crystals for 2~~.~~5 minutes in FE2+ (2~~.~~5M FE(II)-BFR)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19391621}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3e1m]] is a 12 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=3E1M OCA].~~	+

	==See Also==		==See Also==
	*[[Ferritin\|Ferritin]]		*[[Ferritin\|Ferritin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019391621<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Brun, N Le.]]		[[Category: Brun, N Le.]]

OCA at 13:43, 20 October 2012

2012-10-20T13:43:54Z

←Older revision		Revision as of 13:43, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3e1m]] is a 12 chain structure ~~of [[Ferritin]]~~ 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=3E1M OCA].	+	[[3e1m]] is a 12 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=3E1M OCA].

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

OCA: Protected "3e1m" [edit=sysop:move=sysop]

2012-07-26T12:55:20Z

Protected "3e1m" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:55, 26 July 2012

OCA at 12:55, 26 July 2012

2012-07-26T12:55:18Z

←Older revision		Revision as of 12:55, 26 July 2012
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-	{{Seed}}
	[[Image:3e1m.png\|left\|200px]]		[[Image:3e1m.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3e1m", 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_3e1m\| PDB=3e1m \| SCENE= }}		{{STRUCTURE_3e1m\| PDB=3e1m \| SCENE= }}

	===Crystal structure of E. coli Bacterioferritin (BFR) obtained after soaking APO-BFR crystals for 2.5 minutes in FE2+ (2.5M FE(II)-BFR)===		===Crystal structure of E. coli Bacterioferritin (BFR) obtained after soaking APO-BFR crystals for 2.5 minutes in FE2+ (2.5M FE(II)-BFR)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19391621}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19391621 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_19391621}}		{{ABSTRACT_PUBMED_19391621}}

	==About this Structure==		==About this Structure==
-	~~3E1M~~ is a 12 ~~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=3E1M OCA].	+	[[3e1m]] is a 12 chain structure of [[Ferritin]] 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=3E1M OCA].
		+
		+	==See Also==
		+	*[[Ferritin\|Ferritin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19391621~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019391621</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Brun, N Le.]]		[[Category: Brun, N Le.]]
Line 36:		Line 27:
	[[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 May 27 14:37:44 2009''

OCA at 11:37, 27 May 2009

2009-05-27T11:37:44Z

←Older revision		Revision as of 11:37, 27 May 2009
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3e1m.~~jpg~~\|left\|200px]]	+	[[Image:3e1m.png\|left\|200px]]

	<!--		<!--
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	===Crystal structure of E. coli Bacterioferritin (BFR) obtained after soaking APO-BFR crystals for 2.5 minutes in FE2+ (2.5M FE(II)-BFR)===		===Crystal structure of E. coli Bacterioferritin (BFR) obtained after soaking APO-BFR crystals for 2.5 minutes in FE2+ (2.5M FE(II)-BFR)===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19391621}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19391621 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19391621}}

	==About this Structure==		==About this Structure==
	3E1M is a 12 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=3E1M OCA].		3E1M is a 12 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=3E1M OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19391621</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Brun, N Le.]]		[[Category: Brun, N Le.]]
Line 28:		Line 37:
	[[Category: Metal-binding]]		[[Category: Metal-binding]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May ~~6 11~~:28:13 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 27 14:37:44 2009''