7jrq - Revision history

OCA at 15:10, 18 October 2023

OCA — Wed, 18 Oct 2023 15:10:10 GMT

←Older revision		Revision as of 15:10, 18 October 2023
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	<StructureSection load='7jrq' size='340' side='right'caption='[[7jrq]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='7jrq' size='340' side='right'caption='[[7jrq]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7jrq]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JRQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7JRQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7jrq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JRQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JRQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SMU:[5,15-diphenylporphyrinato(2-)-kappa~4~N~21~,N~22~,N~23~,N~24~]manganese'>SMU</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]] 1.75Å</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=7jrq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jrq OCA], [~~http~~://pdbe.org/7jrq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7jrq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7jrq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7jrq ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SMU:[5,15-diphenylporphyrinato(2-)-kappa~4~N~21~,N~22~,N~23~,N~24~]manganese'>SMU</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7jrq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jrq OCA], [https://pdbe.org/7jrq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jrq RCSB], [https://www.ebi.ac.uk/pdbsum/7jrq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jrq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: DeGrado~~, W F~~]]	+	[[Category: DeGrado WF]]
-	[[Category: Mann~~, S I]]~~	+	[[Category: Mann SI]]
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: Helical bundle]]~~	+
-	~~[[Category: High-talent]]~~	+
-	~~[[Category: Metalloprotein]]~~	+
-	~~[[Category: Oxidation]]~~	+
-	~~[[Category: Porphyrin]]~~	+
-	~~[[Category: Sulfoxidation~~]]	+

OCA at 05:56, 20 January 2021

OCA — Wed, 20 Jan 2021 05:56:17 GMT

←Older revision		Revision as of 05:56, 20 January 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7jrq is ~~ON HOLD until Paper~~ Publication	+	==Crystallographically Characterized De Novo Designed Mn-Diphenylporphyrin Binding Protein==
		+	<StructureSection load='7jrq' size='340' side='right'caption='[[7jrq]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7jrq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JRQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7JRQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SMU:[5,15-diphenylporphyrinato(2-)-kappa~4~N~21~,N~22~,N~23~,N~24~]manganese'>SMU</scene></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=7jrq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jrq OCA], [http://pdbe.org/7jrq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jrq RCSB], [http://www.ebi.ac.uk/pdbsum/7jrq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7jrq ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	De novo protein design offers the opportunity to test our understanding of how metalloproteins perform difficult transformations. Attaining high-resolution structural information is critical to understanding how such designs function. There have been many successes in the design of porphyrin-binding proteins; however, crystallographic characterization has been elusive, limiting what can be learned from such studies as well as the extension to new functions. Moreover, formation of highly oxidizing high-valent intermediates poses design challenges that have not been previously implemented: (1) purposeful design of substrate/oxidant access to the binding site and (2) limiting deleterious oxidation of the protein scaffold. Here we report the first crystallographically characterized porphyrin-binding protein that was programmed to not only bind a synthetic Mn-porphyrin but also maintain binding site access to form high-valent oxidation states. We explicitly designed a binding site with accessibility to dioxygen units in the open coordination site of the Mn center. In solution, the protein is capable of accessing a high-valent Mn(V)-oxo species which can transfer an O atom to a thioether substrate. The crystallographic structure is within 0.6 A of the design and indeed contained an aquo ligand with a second water molecule stabilized by hydrogen bonding to a Gln side chain in the active site, offering a structural explanation for the observed reactivity.

-	~~Authors: Mann~~, ~~S.I~~., ~~DeGrado~~, W.F.	+	De Novo Design, Solution Characterization, and Crystallographic Structure of an Abiological Mn-Porphyrin-Binding Protein Capable of Stabilizing a Mn(V) Species.,Mann SI, Nayak A, Gassner GT, Therien MJ, DeGrado WF J Am Chem Soc. 2021 Jan 13;143(1):252-259. doi: 10.1021/jacs.0c10136. Epub 2020, Dec 29. PMID:33373215<ref>PMID:33373215</ref>

-	~~Description: Crystallographically Characterized De Novo Designed Mn~~-~~Diphenylporphyrin Binding Protein~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Mann, S.I]]	+	<div class="pdbe-citations 7jrq" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Degrado, W.F~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
		+	[[Category: DeGrado, W F]]
		+	[[Category: Mann, S I]]
		+	[[Category: De novo protein]]
		+	[[Category: Helical bundle]]
		+	[[Category: High-talent]]
		+	[[Category: Metalloprotein]]
		+	[[Category: Oxidation]]
		+	[[Category: Porphyrin]]
		+	[[Category: Sulfoxidation]]

OCA at 09:03, 23 September 2020

OCA — Wed, 23 Sep 2020 09:03:13 GMT

←Older revision		Revision as of 09:03, 23 September 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7jrq is ON HOLD	+	The entry 7jrq is ON HOLD until Paper Publication

	Authors: Mann, S.I., DeGrado, W.F.		Authors: Mann, S.I., DeGrado, W.F.

OCA: Protected "7jrq" [edit=sysop:move=sysop]

OCA — Wed, 19 Aug 2020 04:57:50 GMT

Protected "7jrq" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:57, 19 August 2020

OCA: New page: '''Unreleased structure''' The entry 7jrq is ON HOLD Authors: Mann, S.I., DeGrado, W.F. Description: Crystallographically Characterized De Novo Designed Mn-Diphenylporphyrin Binding Pr...

OCA — Wed, 19 Aug 2020 04:57:49 GMT

New page: '''Unreleased structure''' The entry 7jrq is ON HOLD Authors: Mann, S.I., DeGrado, W.F. Description: Crystallographically Characterized De Novo Designed Mn-Diphenylporphyrin Binding Pr...

New page

'''Unreleased structure'''

The entry 7jrq is ON HOLD

Authors: Mann, S.I., DeGrado, W.F.

Description: Crystallographically Characterized De Novo Designed Mn-Diphenylporphyrin Binding Protein
[[Category: Unreleased Structures]]
[[Category: Mann, S.I]]
[[Category: Degrado, W.F]]