4psy - Revision history

OCA at 17:22, 20 September 2023

2023-09-20T17:22:04Z

← Older revision		Revision as of 17:22, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4psy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MC4100 Escherichia coli str. K-12 substr. MC4100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PSY FirstGlance]. <br>		<table><tr><td colspan='2'>[[4psy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MC4100 Escherichia coli str. K-12 substr. MC4100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PSY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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]] 0.85Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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=4psy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psy OCA], [https://pdbe.org/4psy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4psy RCSB], [https://www.ebi.ac.uk/pdbsum/4psy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4psy 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=4psy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psy OCA], [https://pdbe.org/4psy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4psy RCSB], [https://www.ebi.ac.uk/pdbsum/4psy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4psy ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:29, 8 February 2023

2023-02-08T07:29:06Z

← Older revision		Revision as of 07:29, 8 February 2023
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	<StructureSection load='4psy' size='340' side='right'caption='[[4psy]], [[Resolution\|resolution]] 0.85Å' scene=''>		<StructureSection load='4psy' size='340' side='right'caption='[[4psy]], [[Resolution\|resolution]] 0.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4psy]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Escherichia_coli_str._k-12_substr.~~_mc4100~~ Escherichia coli str. k-12 substr. ~~mc4100~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4PSY FirstGlance]. <br>		<table><tr><td colspan='2'>[[4psy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MC4100 Escherichia coli str. K-12 substr. MC4100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PSY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>~~</td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</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=4psy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psy OCA], [https://pdbe.org/4psy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4psy RCSB], [https://www.ebi.ac.uk/pdbsum/4psy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4psy ProSAT]</span></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pss\|4pss]]</td></tr>~~
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BN896_0046, folA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1403831 Escherichia coli str. K-12 substr. MC4100])</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=4psy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psy OCA], [~~http~~://pdbe.org/4psy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4psy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4psy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4psy ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	[[http://www.uniprot.org/uniprot/U6N356_ECOLI U6N356_ECOLI]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis (By similarity).[PIRNR:PIRNR000194]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
	*[[Dihydrofolate reductase\|Dihydrofolate reductase]]		*[[Dihydrofolate reductase 3D structures\|Dihydrofolate reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli str. k-12 substr. ~~mc4100~~]]		[[Category: Escherichia coli str. K-12 substr. MC4100]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bennet~~, B C~~]]		[[Category: Bennet BC]]
	[[Category: Dealwis, C]]		[[Category: Dealwis C]]
	[[Category: Petsko~~, G A~~]]		[[Category: Petsko GA]]
	[[Category: Ringe, D]]		[[Category: Ringe D]]
	[[Category: Wan, Q]]		[[Category: Wan Q]]
	[[Category: Wilson~~, M A]]~~		[[Category: Wilson MA]]
	~~[[Category: Oxidoreductase]]~~
	~~[[Category: Reductase~~]]

OCA at 07:26, 17 April 2019

2019-04-17T07:26:16Z

← Older revision		Revision as of 07:26, 17 April 2019
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	==100K crystal structure of Escherichia coli dihydrofolate reductase==		==100K crystal structure of Escherichia coli dihydrofolate reductase==
	<StructureSection load='4psy' size='340' side='right' caption='[[4psy]], [[Resolution\|resolution]] 0.85Å' scene=''>		<StructureSection load='4psy' size='340' side='right'caption='[[4psy]], [[Resolution\|resolution]] 0.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4psy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PSY FirstGlance]. <br>		<table><tr><td colspan='2'>[[4psy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_str._k-12_substr._mc4100 Escherichia coli str. k-12 substr. mc4100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PSY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pss\|4pss]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pss\|4pss]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BN896_0046, folA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1403831 Escherichia coli str. K-12 substr. MC4100])</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=4psy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psy OCA], [http://pdbe.org/4psy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4psy RCSB], [http://www.ebi.ac.uk/pdbsum/4psy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4psy 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=4psy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psy OCA], [http://pdbe.org/4psy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4psy RCSB], [http://www.ebi.ac.uk/pdbsum/4psy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4psy ProSAT]</span></td></tr>
	</table>		</table>
Line 27:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Escherichia coli str. k-12 substr. mc4100]]
			[[Category: Large Structures]]
	[[Category: Bennet, B C]]		[[Category: Bennet, B C]]
	[[Category: Dealwis, C]]		[[Category: Dealwis, C]]

OCA at 22:48, 4 August 2016

2016-08-04T22:48:44Z

← Older revision		Revision as of 22:48, 4 August 2016
Line 1:		Line 1:

	==100K crystal structure of Escherichia coli dihydrofolate reductase==		==100K crystal structure of Escherichia coli dihydrofolate reductase==
	<StructureSection load='4psy' size='340' side='right' caption='[[4psy]], [[Resolution\|resolution]] 0.85Å' scene=''>		<StructureSection load='4psy' size='340' side='right' caption='[[4psy]], [[Resolution\|resolution]] 0.85Å' scene=''>
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	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pss\|4pss]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pss\|4pss]]</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=4psy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4psy RCSB], [http://www.ebi.ac.uk/pdbsum/4psy 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=4psy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psy OCA], [http://pdbe.org/4psy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4psy RCSB], [http://www.ebi.ac.uk/pdbsum/4psy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4psy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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 4psy" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Dihydrofolate reductase\|Dihydrofolate reductase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:23, 24 December 2014

2014-12-24T20:23:19Z

← Older revision		Revision as of 20:23, 24 December 2014
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	<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=4psy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4psy RCSB], [http://www.ebi.ac.uk/pdbsum/4psy 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=4psy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4psy RCSB], [http://www.ebi.ac.uk/pdbsum/4psy PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/U6N356_ECOLI U6N356_ECOLI]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis (By similarity).[PIRNR:PIRNR000194]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 09:07, 17 December 2014

2014-12-17T09:07:47Z

← Older revision		Revision as of 09:07, 17 December 2014
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	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	~~Most macromolecular X~~-~~ray structures are determined from cryocooled crystals~~, ~~but it is unclear whether cryocooling distorts functionally relevant flexibility. Here~~ we ~~compare independently acquired pairs of high~~-resolution ~~data sets~~ of ~~a model~~ Michaelis complex of ~~dihydrofolate reductase (~~DHFR~~), collected by separate groups at both room~~ and ~~cryogenic temperatures~~. ~~These~~ data ~~sets allow us~~ to ~~isolate the differences between experimental procedures and between temperatures~~. ~~Our analyses of multiconformer models and time~~-~~averaged ensembles suggest that cryocooling suppresses and otherwise modifies side~~-~~chain and main~~-~~chain conformational heterogeneity~~, ~~quenching dynamic contact networks~~. ~~Despite some idiosyncratic differences, most changes from room temperature~~ to ~~cryogenic temperature are conserved and likely reflect temperature~~-~~dependent solvent remodeling~~. ~~Both cryogenic data sets point~~ to ~~additional conformations not evident in~~ the ~~corresponding room temperature data sets~~, suggesting that ~~cryocooling does not merely trap preexisting~~ conformational ~~heterogeneity~~. ~~Our results demonstrate~~ that ~~crystal cryocooling consistently distorts~~ the ~~energy landscape~~ of ~~DHFR~~, ~~a paragon for understanding functional protein dynamics~~.		Dihydrofolate reductase (DHFR) catalyzes the NADPH-dependent reduction of dihydrofolate (DHF) to tetrahydrofolate (THF). An important step in the mechanism involves proton donation to the N5 atom of DHF. The inability to determine the protonation states of active site residues and substrate has led to a lack of consensus regarding the catalytic mechanism involved. To resolve this ambiguity, we conducted neutron and ultrahigh-resolution X-ray crystallographic studies of the pseudo-Michaelis ternary complex of Escherichia coli DHFR with folate and NADP+. The neutron data were collected to 2.0-A resolution using a 3.6-mm3 crystal with the quasi-Laue technique. The structure reveals that the N3 atom of folate is protonated, whereas Asp27 is negatively charged. Previous mechanisms have proposed a keto-to-enol tautomerization of the substrate to facilitate protonation of the N5 atom. The structure supports the existence of the keto tautomer owing to protonation of the N3 atom, suggesting that tautomerization is unnecessary for catalysis. In the 1.05-A resolution X-ray structure of the ternary complex, conformational disorder of the Met20 side chain is coupled to electron density for a partially occupied water within hydrogen-bonding distance of the N5 atom of folate; this suggests direct protonation of substrate by solvent. We propose a catalytic mechanism for DHFR that involves stabilization of the keto tautomer of the substrate, elevation of the pKa value of the N5 atom of DHF by Asp27, and protonation of N5 by water that gains access to the active site through fluctuation of the Met20 side chain even though the Met20 loop is closed.

	~~Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex~~ of ~~DHFR~~.,~~Keedy DA~~, ~~van den Bedem H~~, ~~Sivak DA~~, ~~Petsko GA~~, ~~Ringe D~~, ~~Wilson MA~~, ~~Fraser JS Structure~~. 2014 ~~Jun 10;22(6):899-910~~. ~~doi~~: ~~10.1016/j.str.2014.04.016. Epub 2014, May 29~~. PMID:~~24882744~~<ref>PMID:~~24882744~~</ref>		Toward resolving the catalytic mechanism of dihydrofolate reductase using neutron and ultrahigh-resolution X-ray crystallography.,Wan Q, Bennett BC, Wilson MA, Kovalevsky A, Langan P, Howell EE, Dealwis C Proc Natl Acad Sci U S A. 2014 Dec 1. pii: 201415856. PMID:25453083<ref>PMID:25453083</ref>

	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>

OCA at 10:43, 19 November 2014

2014-11-19T10:43:08Z

← Older revision		Revision as of 10:43, 19 November 2014
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[4psy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PSY FirstGlance]. <br>		<table><tr><td colspan='2'>[[4psy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PSY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~CSW~~:~~CYSTEINE~~-~~S-DIOXIDE~~'>~~CSW~~</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pss\|4pss]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pss\|4pss]]</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=4psy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4psy RCSB], [http://www.ebi.ac.uk/pdbsum/4psy 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=4psy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4psy RCSB], [http://www.ebi.ac.uk/pdbsum/4psy PDBsum]</span></td></tr>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Bennet, B C.]]		[[Category: Bennet, B C]]
	[[Category: Dealwis, C.]]		[[Category: Dealwis, C]]
	[[Category: Petsko, G A.]]		[[Category: Petsko, G A]]
	[[Category: Ringe, D.]]		[[Category: Ringe, D]]
	[[Category: Wan, Q.]]		[[Category: Wan, Q]]
	[[Category: Wilson, M A.]]		[[Category: Wilson, M A]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Reductase]]		[[Category: Reductase]]

OCA at 08:48, 20 October 2014

2014-10-20T08:48:20Z

← Older revision		Revision as of 08:48, 20 October 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4psy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PSY FirstGlance]. <br>		<table><tr><td colspan='2'>[[4psy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PSY FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSW:CYSTEINE-S-DIOXIDE'>CSW</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSW:CYSTEINE-S-DIOXIDE'>CSW</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pss\|4pss]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pss\|4pss]]</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=4psy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4psy RCSB], [http://www.ebi.ac.uk/pdbsum/4psy 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=4psy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4psy RCSB], [http://www.ebi.ac.uk/pdbsum/4psy PDBsum]</span></td></tr>
	<table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 09:17, 16 July 2014

2014-07-16T09:17:01Z

← Older revision		Revision as of 09:17, 16 July 2014
Line 2:		Line 2:
	<StructureSection load='4psy' size='340' side='right' caption='[[4psy]], [[Resolution\|resolution]] 0.85Å' scene=''>		<StructureSection load='4psy' size='340' side='right' caption='[[4psy]], [[Resolution\|resolution]] 0.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4psy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSY OCA]. <br>		<table><tr><td colspan='2'>[[4psy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PSY FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene><br>		</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene><br>
	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSW:CYSTEINE-S-DIOXIDE'>CSW</scene></td></tr>		<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSW:CYSTEINE-S-DIOXIDE'>CSW</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pss\|4pss]]</td></tr>		<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pss\|4pss]]</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></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=4psy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4psy RCSB], [http://www.ebi.ac.uk/pdbsum/4psy PDBsum]</span></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=4psy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4psy RCSB], [http://www.ebi.ac.uk/pdbsum/4psy PDBsum]</span></td></tr>
	<table>		<table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Most macromolecular X-ray structures are determined from cryocooled crystals, but it is unclear whether cryocooling distorts functionally relevant flexibility. Here we compare independently acquired pairs of high-resolution data sets of a model Michaelis complex of dihydrofolate reductase (DHFR), collected by separate groups at both room and cryogenic temperatures. These data sets allow us to isolate the differences between experimental procedures and between temperatures. Our analyses of multiconformer models and time-averaged ensembles suggest that cryocooling suppresses and otherwise modifies side-chain and main-chain conformational heterogeneity, quenching dynamic contact networks. Despite some idiosyncratic differences, most changes from room temperature to cryogenic temperature are conserved and likely reflect temperature-dependent solvent remodeling. Both cryogenic data sets point to additional conformations not evident in the corresponding room temperature data sets, suggesting that cryocooling does not merely trap preexisting conformational heterogeneity. Our results demonstrate that crystal cryocooling consistently distorts the energy landscape of DHFR, a paragon for understanding functional protein dynamics.

			Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex of DHFR.,Keedy DA, van den Bedem H, Sivak DA, Petsko GA, Ringe D, Wilson MA, Fraser JS Structure. 2014 Jun 10;22(6):899-910. doi: 10.1016/j.str.2014.04.016. Epub 2014, May 29. PMID:24882744<ref>PMID:24882744</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:28, 14 May 2014

2014-05-14T07:28:58Z

← Older revision		Revision as of 07:28, 14 May 2014
Line 1:		Line 1:
	'''~~Unreleased structure~~'''		==100K crystal structure of Escherichia coli dihydrofolate reductase==
			<StructureSection load='4psy' size='340' side='right' caption='[[4psy]], [[Resolution\|resolution]] 0.85Å' scene=''>
	~~The entry~~ 4psy is ~~ON HOLD until Paper Publication~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[4psy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSY OCA]. <br>
	~~Authors~~: ~~Wilson~~, M.A., ~~Wan~~, Q., Bennet, B.C., Dealwis, C., Ringe, D., ~~Petsko~~, G.A.		</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene><br>
			<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSW:CYSTEINE-S-DIOXIDE'>CSW</scene></td></tr>
	~~Description~~: ~~100K crystal structure of Escherichia coli dihydrofolate reductase~~		<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pss\|4pss]]</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></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=4psy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4psy RCSB], [http://www.ebi.ac.uk/pdbsum/4psy PDBsum]</span></td></tr>
			<table>
			__TOC__
			</StructureSection>
			[[Category: Bennet, B C.]]
			[[Category: Dealwis, C.]]
			[[Category: Petsko, G A.]]
			[[Category: Ringe, D.]]
			[[Category: Wan, Q.]]
			[[Category: Wilson, M A.]]
			[[Category: Oxidoreductase]]
			[[Category: Reductase]]