4i3a - Revision history

OCA at 08:38, 9 November 2022

OCA — Wed, 09 Nov 2022 08:38:21 GMT

←Older revision		Revision as of 08:38, 9 November 2022
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	==Structures of PR1 and PR2 intermediates from time-resolved laue crystallography collected at 14ID-B, APS==		==Structures of PR1 and PR2 intermediates from time-resolved laue crystallography collected at 14ID-B, APS==
-	<StructureSection load='4i3a' size='340' side='right' caption='[[4i3a]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='4i3a' size='340' side='right'caption='[[4i3a]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4i3a]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Dsm_244 Dsm 244~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I3A OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4I3A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4i3a]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I3A FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4hy8\|4hy8]], [[4i38\|4i38]], [[4i39\|4i39]], [[4i3i\|4i3i]], [[4i3j\|4i3j]], [[3ve3\|3ve3]], [[3ve4\|3ve4]], [[1ts0\|1ts0]], [[1ts6\|1ts6]], [[1ts7\|1ts7]], [[1ts8\|1ts8]]</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=4i3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i3a OCA], [https://pdbe.org/4i3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i3a RCSB], [https://www.ebi.ac.uk/pdbsum/4i3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i3a ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053 DSM 244])~~</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=4i3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i3a OCA], [~~http~~://pdbe.org/4i3a PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4i3a RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4i3a PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4i3a ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA]] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.	+	[https://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dsm 244~~]]	+	[[Category: Halorhodospira halophila]]
-	[[Category: Ihee, H]]	+	[[Category: Large Structures]]
-	[[Category: Jung~~, Y O~~]]	+	[[Category: Ihee H]]
-	[[Category: Kim, J]]	+	[[Category: Jung YO]]
-	[[Category: Lee~~, J H~~]]	+	[[Category: Kim J]]
-	[[Category: Moffat, K]]	+	[[Category: Lee JH]]
-	[[Category: Schmidt, M]]	+	[[Category: Moffat K]]
-	[[Category: Vukica, S]]	+	[[Category: Schmidt M]]
-	~~[[Category: Chromophore]]~~	+	[[Category: Vukica S]]
-	~~[[Category: Luminescent protein]]~~	+
-	~~[[Category: Photoreceptor]]~~	+
-	~~[[Category: Photoreceptor protein]]~~	+
-	~~[[Category: Receptor]]~~	+
-	~~[[Category: Sensory transduction~~]]	+

OCA at 15:54, 4 August 2016

OCA — Thu, 04 Aug 2016 15:54:10 GMT

←Older revision		Revision as of 15:54, 4 August 2016
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		+
	==Structures of PR1 and PR2 intermediates from time-resolved laue crystallography collected at 14ID-B, APS==		==Structures of PR1 and PR2 intermediates from time-resolved laue crystallography collected at 14ID-B, APS==
	<StructureSection load='4i3a' size='340' side='right' caption='[[4i3a]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='4i3a' size='340' side='right' caption='[[4i3a]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4hy8\|4hy8]], [[4i38\|4i38]], [[4i39\|4i39]], [[4i3i\|4i3i]], [[4i3j\|4i3j]], [[3ve3\|3ve3]], [[3ve4\|3ve4]], [[1ts0\|1ts0]], [[1ts6\|1ts6]], [[1ts7\|1ts7]], [[1ts8\|1ts8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4hy8\|4hy8]], [[4i38\|4i38]], [[4i39\|4i39]], [[4i3i\|4i3i]], [[4i3j\|4i3j]], [[3ve3\|3ve3]], [[3ve4\|3ve4]], [[1ts0\|1ts0]], [[1ts6\|1ts6]], [[1ts7\|1ts7]], [[1ts8\|1ts8]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053 DSM 244])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053 DSM 244])</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=4i3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i3a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i3a RCSB], [http://www.ebi.ac.uk/pdbsum/4i3a 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=4i3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i3a OCA], [http://pdbe.org/4i3a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4i3a RCSB], [http://www.ebi.ac.uk/pdbsum/4i3a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4i3a ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4i3a" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:45, 25 December 2014

OCA — Thu, 25 Dec 2014 10:45:31 GMT

←Older revision		Revision as of 10:45, 25 December 2014
Line 8:		Line 8:
	<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=4i3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i3a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i3a RCSB], [http://www.ebi.ac.uk/pdbsum/4i3a 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=4i3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i3a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i3a RCSB], [http://www.ebi.ac.uk/pdbsum/4i3a PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA]] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 16:56, 10 December 2014

OCA — Wed, 10 Dec 2014 16:56:41 GMT

←Older revision		Revision as of 16:56, 10 December 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structures of PR1 and PR2 intermediates from time-resolved laue crystallography collected at 14ID-B, APS==
		+	<StructureSection load='4i3a' size='340' side='right' caption='[[4i3a]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4i3a]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_244 Dsm 244]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I3A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I3A FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4hy8\|4hy8]], [[4i38\|4i38]], [[4i39\|4i39]], [[4i3i\|4i3i]], [[4i3j\|4i3j]], [[3ve3\|3ve3]], [[3ve4\|3ve4]], [[1ts0\|1ts0]], [[1ts6\|1ts6]], [[1ts7\|1ts7]], [[1ts8\|1ts8]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053 DSM 244])</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=4i3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i3a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i3a RCSB], [http://www.ebi.ac.uk/pdbsum/4i3a PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Trans-to-cis isomerization, the key reaction in photoactive proteins, usually cannot occur through the standard one-bond-flip mechanism. Owing to spatial constraints imposed by a protein environment, isomerization probably proceeds through a volume-conserving mechanism in which highly choreographed atomic motions are expected, the details of which have not yet been observed directly. Here we employ time-resolved X-ray crystallography to visualize structurally the isomerization of the p-coumaric acid chromophore in photoactive yellow protein with a time resolution of 100 ps and a spatial resolution of 1.6 A. The structure of the earliest intermediate (I(T)) resembles a highly strained transition state in which the torsion angle is located halfway between the trans- and cis-isomers. The reaction trajectory of I(T) bifurcates into two structurally distinct cis intermediates via hula-twist and bicycle-pedal pathways. The bifurcating reaction pathways can be controlled by weakening the hydrogen bond between the chromophore and an adjacent residue through E46Q mutation, which switches off the bicycle-pedal pathway.

-	~~The entry 4i3a is ON HOLD until Paper Publication~~	+	Volume-conserving trans-cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography.,Jung YO, Lee JH, Kim J, Schmidt M, Moffat K, Srajer V, Ihee H Nat Chem. 2013 Mar;5(3):212-20. doi: 10.1038/nchem.1565. Epub 2013 Feb 3. PMID:23422563<ref>PMID:23422563</ref>

-	~~Authors~~: Jung, Y.O., Lee, J.H~~., Kim, J.~~, Schmidt, M., Vukica, S~~., Moffat, K., Ihee, H.~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Structures of PR1 and PR2 intermediates from time-resolved laue crystallography collected at 14ID-B, APS~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dsm 244]]
		+	[[Category: Ihee, H]]
		+	[[Category: Jung, Y O]]
		+	[[Category: Kim, J]]
		+	[[Category: Lee, J H]]
		+	[[Category: Moffat, K]]
		+	[[Category: Schmidt, M]]
		+	[[Category: Vukica, S]]
		+	[[Category: Chromophore]]
		+	[[Category: Luminescent protein]]
		+	[[Category: Photoreceptor]]
		+	[[Category: Photoreceptor protein]]
		+	[[Category: Receptor]]
		+	[[Category: Sensory transduction]]

OCA at 13:43, 6 March 2013

OCA — Wed, 06 Mar 2013 13:43:40 GMT

←Older revision		Revision as of 13:43, 6 March 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4i3a is ON HOLD	+	The entry 4i3a is ON HOLD until Paper Publication

	Authors: Jung, Y.O., Lee, J.H., Kim, J., Schmidt, M., Vukica, S., Moffat, K., Ihee, H.		Authors: Jung, Y.O., Lee, J.H., Kim, J., Schmidt, M., Vukica, S., Moffat, K., Ihee, H.

	Description: Structures of PR1 and PR2 intermediates from time-resolved laue crystallography collected at 14ID-B, APS		Description: Structures of PR1 and PR2 intermediates from time-resolved laue crystallography collected at 14ID-B, APS

OCA at 20:47, 12 December 2012

OCA — Wed, 12 Dec 2012 20:47:03 GMT

←Older revision		Revision as of 20:47, 12 December 2012
Line 3:		Line 3:
	The entry 4i3a is ON HOLD		The entry 4i3a is ON HOLD

-	Authors: Y.O.~~JUNG~~, J.H.~~LEE~~, J.~~KIM~~, M.~~SCHMIDT~~, S.~~VUKICA~~, K.~~MOFFAT~~, H.~~IHEE~~	+	Authors: Jung, Y.O., Lee, J.H., Kim, J., Schmidt, M., Vukica, S., Moffat, K., Ihee, H.

-	Description: ~~STRUCTURES OF~~ PR1 ~~AND~~ PR2 ~~INTERMEDIATES FROM TIME~~-~~RESOLVED LAUE CRYSTALLOGRAPHY COLLECTED AT~~ 14ID-B, APS	+	Description: Structures of PR1 and PR2 intermediates from time-resolved laue crystallography collected at 14ID-B, APS

OCA: Protected "4i3a" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2012 10:32:44 GMT

Protected "4i3a" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:32, 5 December 2012

OCA: New page: '''Unreleased structure''' The entry 4i3a is ON HOLD Authors: Y.O.JUNG, J.H.LEE, J.KIM, M.SCHMIDT, S.VUKICA, K.MOFFAT, H.IHEE Description: STRUCTURES OF PR1 AND PR2 INTERMEDIATES FROM ...

OCA — Wed, 05 Dec 2012 10:32:43 GMT

New page: '''Unreleased structure''' The entry 4i3a is ON HOLD Authors: Y.O.JUNG, J.H.LEE, J.KIM, M.SCHMIDT, S.VUKICA, K.MOFFAT, H.IHEE Description: STRUCTURES OF PR1 AND PR2 INTERMEDIATES FROM ...

New page

'''Unreleased structure'''

The entry 4i3a is ON HOLD

Authors: Y.O.JUNG, J.H.LEE, J.KIM, M.SCHMIDT, S.VUKICA, K.MOFFAT, H.IHEE

Description: STRUCTURES OF PR1 AND PR2 INTERMEDIATES FROM TIME-RESOLVED LAUE CRYSTALLOGRAPHY COLLECTED AT 14ID-B, APS