6c1j - Revision history

OCA at 14:54, 4 October 2023

OCA — Wed, 04 Oct 2023 14:54:39 GMT

←Older revision		Revision as of 14:54, 4 October 2023
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	<StructureSection load='6c1j' size='340' side='right'caption='[[6c1j]], [[Resolution\|resolution]] 1.06Å' scene=''>		<StructureSection load='6c1j' size='340' side='right'caption='[[6c1j]], [[Resolution\|resolution]] 1.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6c1j]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C1J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6C1J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6c1j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C1J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6C1J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CL:CHLORIDE+ION'~~>~~CL</scene>, <scene name='pdbligand=DNX:3,4~~-~~DINITROPHENOL'>DNX</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.063Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ksi ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~303~~ "~~Bacillus fluorescens putidus~~" ~~Flugge 1886])~~<~~/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=DNX:3,4-DINITROPHENOL'>DNX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Steroid_Delta-isomerase Steroid Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.1 5.3.3.1]~~ </~~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=6c1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c1j OCA], [https://pdbe.org/6c1j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6c1j RCSB], [https://www.ebi.ac.uk/pdbsum/6c1j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6c1j ProSAT]</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=6c1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c1j OCA], [~~http~~://pdbe.org/6c1j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6c1j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6c1j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6c1j ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SDIS_PSEPU SDIS_PSEPU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus fluorescens putidus flugge 1886]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Steroid Delta-isomerase~~]]	+	[[Category: Pseudomonas putida]]
-	[[Category: Herschlag, D]]	+	[[Category: Herschlag D]]
-	[[Category: Pinney~~, M M~~]]	+	[[Category: Pinney MM]]
-	[[Category: Yabukarski, F]]	+	[[Category: Yabukarski F]]
-	~~[[Category: Enzyme]]~~	+
-	~~[[Category: Isomerase~~]]	+

OCA at 08:22, 27 November 2019

OCA — Wed, 27 Nov 2019 08:22:14 GMT

←Older revision		Revision as of 08:22, 27 November 2019
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	==Crystal Structure of Ketosteroid Isomerase Y32F/Y57F/D40N mutant from Pseudomonas Putida (pKSI) bound to 3,4-dinitrophenol==		==Crystal Structure of Ketosteroid Isomerase Y32F/Y57F/D40N mutant from Pseudomonas Putida (pKSI) bound to 3,4-dinitrophenol==
-	<StructureSection load='6c1j' size='340' side='right' caption='[[6c1j]], [[Resolution\|resolution]] 1.06Å' scene=''>	+	<StructureSection load='6c1j' size='340' side='right'caption='[[6c1j]], [[Resolution\|resolution]] 1.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6c1j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C1J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C1J FirstGlance]. <br>		<table><tr><td colspan='2'>[[6c1j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C1J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C1J FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus fluorescens putidus flugge 1886]]		[[Category: Bacillus fluorescens putidus flugge 1886]]
		+	[[Category: Large Structures]]
	[[Category: Steroid Delta-isomerase]]		[[Category: Steroid Delta-isomerase]]
	[[Category: Herschlag, D]]		[[Category: Herschlag, D]]

OCA at 06:34, 22 August 2018

OCA — Wed, 22 Aug 2018 06:34:06 GMT

←Older revision		Revision as of 06:34, 22 August 2018
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	<StructureSection load='6c1j' size='340' side='right' caption='[[6c1j]], [[Resolution\|resolution]] 1.06Å' scene=''>		<StructureSection load='6c1j' size='340' side='right' caption='[[6c1j]], [[Resolution\|resolution]] 1.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6c1j]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C1J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C1J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6c1j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C1J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C1J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DNX:3,4-DINITROPHENOL'>DNX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DNX:3,4-DINITROPHENOL'>DNX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksi ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Steroid_Delta-isomerase Steroid Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.1 5.3.3.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Steroid_Delta-isomerase Steroid Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.1 5.3.3.1] </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=6c1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c1j OCA], [http://pdbe.org/6c1j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c1j RCSB], [http://www.ebi.ac.uk/pdbsum/6c1j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c1j ProSAT]</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=6c1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c1j OCA], [http://pdbe.org/6c1j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c1j RCSB], [http://www.ebi.ac.uk/pdbsum/6c1j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c1j ProSAT]</span></td></tr>
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	</div>		</div>
	<div class="pdbe-citations 6c1j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6c1j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ketosteroid Isomerase\|Ketosteroid Isomerase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus fluorescens putidus flugge 1886]]
	[[Category: Steroid Delta-isomerase]]		[[Category: Steroid Delta-isomerase]]
	[[Category: Herschlag, D]]		[[Category: Herschlag, D]]

OCA at 07:14, 25 July 2018

OCA — Wed, 25 Jul 2018 07:14:08 GMT

←Older revision		Revision as of 07:14, 25 July 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 6c1j is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of Ketosteroid Isomerase Y32F/Y57F/D40N mutant from Pseudomonas Putida (pKSI) bound to 3,4-dinitrophenol==
		+	<StructureSection load='6c1j' size='340' side='right' caption='[[6c1j]], [[Resolution\|resolution]] 1.06Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6c1j]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C1J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C1J FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DNX:3,4-DINITROPHENOL'>DNX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Steroid_Delta-isomerase Steroid Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.1 5.3.3.1] </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=6c1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c1j OCA], [http://pdbe.org/6c1j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c1j RCSB], [http://www.ebi.ac.uk/pdbsum/6c1j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c1j ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Hydrogen bonds are fundamental to biological systems and are regularly found in networks implicated in folding, molecular recognition, catalysis, and allostery. Given their ubiquity, we asked the fundamental questions of whether, and to what extent, hydrogen bonds within networks are structurally coupled. To address these questions, we turned to three protein systems, two variants of ketosteroid isomerase and one of photoactive yellow protein. We perturbed their hydrogen bond networks via a combination of site-directed mutagenesis and unnatural amino acid substitution, and we used 1H NMR and high-resolution X-ray crystallography to determine the effects of these perturbations on the lengths of the two oxyanion hole hydrogen bonds that are donated to negatively-charged transition state analogs. Perturbations that lengthened or shortened one of the oxyanion hole hydrogen bonds had the opposite effect on the other. The oxyanion hole hydrogen bonds were also affected by distal hydrogen bonds in the network, with smaller perturbations for more remote hydrogen bonds. Across 19 measurements in three systems, the length change in one oxyanion hole hydrogen bond was propagated to the other, by a factor of -0.30 +/- 0.03. This common effect suggests that hydrogen bond coupling is minimally influenced by the remaining protein scaffold. The observed coupling is reproduced by molecular mechanics and quantum mechanics/molecular mechanics (QM/MM) calculations for changes to a proximal oxyanion hole hydrogen bond. However, effects from distal hydrogen bonds are reproduced only by QM/MM, suggesting the importance of polarization in hydrogen bond coupling. These results deepen our understanding of hydrogen bonds and their networks, providing strong evidence for long-range coupling and to the extent of this coupling. We provide a broadly predictive quantitative relationship that can be applied to and can be further tested in new systems.

-	~~Authors:~~ Yabukarski, F., ~~Pinney~~, ~~M.M.~~, ~~Herschlag~~, D.	+	Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein.,Pinney M, Natarajan A, Yabukarski F, Sanchez DM, Liu F, Liang R, Doukov TI, Schwans JP, Martinez TJ, Herschlag D J Am Chem Soc. 2018 Jul 10. doi: 10.1021/jacs.8b01596. PMID:29990421<ref>PMID:29990421</ref>

-	~~Description: Crystal Structure of Ketosteroid Isomerase Y32F~~/~~Y57F/D40N mutant from Pseudomonas Putida (pKSI) bound to 3~~,~~4-dinitrophenol~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Pinney, M.M~~]]	+	<div class="pdbe-citations 6c1j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Steroid Delta-isomerase]]
	[[Category: Herschlag, D]]		[[Category: Herschlag, D]]
		+	[[Category: Pinney, M M]]
	[[Category: Yabukarski, F]]		[[Category: Yabukarski, F]]
		+	[[Category: Enzyme]]
		+	[[Category: Isomerase]]

OCA at 05:07, 7 February 2018

OCA — Wed, 07 Feb 2018 05:07:03 GMT

←Older revision		Revision as of 05:07, 7 February 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6c1j is ON HOLD	+	The entry 6c1j is ON HOLD until Paper Publication

	Authors: Yabukarski, F., Pinney, M.M., Herschlag, D.		Authors: Yabukarski, F., Pinney, M.M., Herschlag, D.

OCA: Protected "6c1j" [edit=sysop:move=sysop]

OCA — Wed, 10 Jan 2018 07:15:12 GMT

Protected "6c1j" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:15, 10 January 2018

OCA: New page: '''Unreleased structure''' The entry 6c1j is ON HOLD Authors: Yabukarski, F., Pinney, M.M., Herschlag, D. Description: Crystal Structure of Ketosteroid Isomerase Y32F/Y57F/D40N mutant ...

OCA — Wed, 10 Jan 2018 07:15:10 GMT

New page: '''Unreleased structure''' The entry 6c1j is ON HOLD Authors: Yabukarski, F., Pinney, M.M., Herschlag, D. Description: Crystal Structure of Ketosteroid Isomerase Y32F/Y57F/D40N mutant ...

New page

'''Unreleased structure'''

The entry 6c1j is ON HOLD

Authors: Yabukarski, F., Pinney, M.M., Herschlag, D.

Description: Crystal Structure of Ketosteroid Isomerase Y32F/Y57F/D40N mutant from Pseudomonas Putida (pKSI) bound to 3,4-dinitrophenol
[[Category: Unreleased Structures]]
[[Category: Pinney, M.M]]
[[Category: Herschlag, D]]
[[Category: Yabukarski, F]]