5wlk - Revision history

OCA at 14:16, 4 October 2023

2023-10-04T14:16:26Z

←Older revision		Revision as of 14:16, 4 October 2023
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	<StructureSection load='5wlk' size='340' side='right'caption='[[5wlk]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5wlk' size='340' side='right'caption='[[5wlk]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wlk]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WLK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5WLK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wlk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WLK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WLK FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ZN:ZINC+ION'>ZN</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]] 1.8Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5wlk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wlk OCA], [~~http~~://pdbe.org/5wlk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5wlk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5wlk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5wlk 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=5wlk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wlk OCA], [https://pdbe.org/5wlk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wlk RCSB], [https://www.ebi.ac.uk/pdbsum/5wlk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wlk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~DeGrado, W F~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Liu, L~~]]	+	[[Category: DeGrado WF]]
-	[[Category: ~~Zhang, S Q~~]]	+	[[Category: Liu L]]
-	[[Category: ~~De novo protein]]~~	+	[[Category: Zhang S-Q]]
-	~~[[Category: Helical bundle]]~~	+
-	~~[[Category: Metal binding]]~~	+
-	~~[[Category: Protein design~~]]	+

OCA at 09:56, 1 January 2020

2020-01-01T09:56:13Z

←Older revision		Revision as of 09:56, 1 January 2020
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	==De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH2==		==De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH2==
-	<StructureSection load='5wlk' size='340' side='right' caption='[[5wlk]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5wlk' size='340' side='right'caption='[[5wlk]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5wlk]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WLK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WLK FirstGlance]. <br>		<table><tr><td colspan='2'>[[5wlk]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WLK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WLK FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: DeGrado, W F]]		[[Category: DeGrado, W F]]
	[[Category: Liu, L]]		[[Category: Liu, L]]

OCA at 05:49, 3 January 2018

2018-01-03T05:49:13Z

←Older revision		Revision as of 05:49, 3 January 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5wlk is ~~ON HOLD until Paper~~ Publication	+	==De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH2==
		+	<StructureSection load='5wlk' size='340' side='right' caption='[[5wlk]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5wlk]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WLK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WLK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></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=5wlk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wlk OCA], [http://pdbe.org/5wlk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wlk RCSB], [http://www.ebi.ac.uk/pdbsum/5wlk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wlk ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	De novo design provides an attractive approach to test the mechanism by which metalloproteins define the geometry and reactivity of their metal ion cofactors. While there has been considerable progress in designing proteins that bind transition metal ions including iron-sulphur clusters, the design of tetranuclear clusters with oxygen-rich environments has not been accomplished. Here, we describe the design of tetranuclear clusters, consisting of four Zn(2+) and four carboxylate oxygens situated at the vertices of a distorted cube-like structure. The tetra-Zn(2+) clusters are bound at a buried site within a four-helix bundle, with each helix donating a single carboxylate (Glu or Asp) and imidazole (His) ligand, as well as second- and third-shell ligands. Overall, the designed site consists of four Zn(2+) and 16 polar sidechains in a fully connected hydrogen-bonded network. The designed proteins have apolar cores at the top and bottom of the bundle, which drive the assembly of the liganding residues near the center of the bundle. The steric bulk of the apolar residues surrounding the binding site was varied to determine how subtle changes in helix-helix packing affect the binding site. The crystal structures of two of four proteins synthesized were in good agreement with the overall design; both formed a distorted cuboidal site stabilized by flanking second and third-shell interactions that stabilize the primary ligands. A third structure bound a single Zn(2+) in an unanticipated geometry and the fourth bound multiple Zn(2+) at multiple sites at partial occupancy. The metal-binding and conformational properties of the helical bundles in solution, probed by circular dichroism spectroscopy, analytical ultracentrifugation and NMR, were consistent with the crystal structures.

-	~~Authors: Zhang, S.~~-Q., ~~Liu~~, L., DeGrado, W.F.	+	De Novo Design of Tetranuclear Transition Metal Clusters Stabilized by Hydrogen-Bonded Networks in Helical Bundles.,Zhang SQ, Chino M, Liu L, Tang Y, Hu X, DeGrado WF, Lombardi A J Am Chem Soc. 2017 Dec 18. doi: 10.1021/jacs.7b08261. PMID:29249157<ref>PMID:29249157</ref>

-	~~Description: De Novo Design~~ of ~~Polynuclear Transition Metal Clusters in Helix Bundles~~-~~4EH2~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5wlk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DeGrado, W F]]
	[[Category: Liu, L]]		[[Category: Liu, L]]
-	[[Category: ~~Degrado~~, ~~W.F~~]]	+	[[Category: Zhang, S Q]]
-	[[Category: ~~Zhang, S.-Q~~]]	+	[[Category: De novo protein]]
		+	[[Category: Helical bundle]]
		+	[[Category: Metal binding]]
		+	[[Category: Protein design]]

OCA at 05:20, 11 October 2017

2017-10-11T05:20:10Z

←Older revision		Revision as of 05:20, 11 October 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5wlk is ON HOLD	+	The entry 5wlk is ON HOLD until Paper Publication

	Authors: Zhang, S.-Q., Liu, L., DeGrado, W.F.		Authors: Zhang, S.-Q., Liu, L., DeGrado, W.F.

OCA: Protected "5wlk" [edit=sysop:move=sysop]

2017-09-27T14:57:23Z

Protected "5wlk" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:57, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5wlk is ON HOLD Authors: Zhang, S.-Q., Liu, L., DeGrado, W.F. Description: De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles...

2017-09-27T14:57:22Z

New page: '''Unreleased structure''' The entry 5wlk is ON HOLD Authors: Zhang, S.-Q., Liu, L., DeGrado, W.F. Description: De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles...

New page

'''Unreleased structure'''

The entry 5wlk is ON HOLD

Authors: Zhang, S.-Q., Liu, L., DeGrado, W.F.

Description: De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH2
[[Category: Unreleased Structures]]
[[Category: Liu, L]]
[[Category: Degrado, W.F]]
[[Category: Zhang, S.-Q]]