5b34 - Revision history

OCA at 10:02, 6 September 2023

OCA — Wed, 06 Sep 2023 10:02:28 GMT

←Older revision		Revision as of 10:02, 6 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5b34]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B34 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B34 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5b34]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B34 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B34 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4QL:2,4,6-TRIS(IODANYL)-5-(OCTANOYLAMINO)BENZENE-1,3-DICARBOXYLIC+ACID'>4QL</scene>, <scene name='pdbligand=D10:DECANE'>D10</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=DD9:NONANE'>DD9</scene>, <scene name='pdbligand=HP6:HEPTANE'>HP6</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=R16:HEXADECANE'>R16</scene>, <scene name='pdbligand=RET:RETINAL'>RET</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]] 2.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4QL:2,4,6-TRIS(IODANYL)-5-(OCTANOYLAMINO)BENZENE-1,3-DICARBOXYLIC+ACID'>4QL</scene>, <scene name='pdbligand=D10:DECANE'>D10</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=DD9:NONANE'>DD9</scene>, <scene name='pdbligand=HP6:HEPTANE'>HP6</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=R16:HEXADECANE'>R16</scene>, <scene name='pdbligand=RET:RETINAL'>RET</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=5b34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b34 OCA], [https://pdbe.org/5b34 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b34 RCSB], [https://www.ebi.ac.uk/pdbsum/5b34 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b34 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=5b34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b34 OCA], [https://pdbe.org/5b34 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b34 RCSB], [https://www.ebi.ac.uk/pdbsum/5b34 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b34 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:37, 31 May 2023

OCA — Wed, 31 May 2023 06:37:19 GMT

←Older revision		Revision as of 06:37, 31 May 2023
Line 3:		Line 3:
	<StructureSection load='5b34' size='340' side='right'caption='[[5b34]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5b34' size='340' side='right'caption='[[5b34]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5b34]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B34 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5B34 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5b34]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B34 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B34 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4QL:2,4,6-TRIS(IODANYL)-5-(OCTANOYLAMINO)BENZENE-1,3-DICARBOXYLIC+ACID'>4QL</scene>, <scene name='pdbligand=D10:DECANE'>D10</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=DD9:NONANE'>DD9</scene>, <scene name='pdbligand=HP6:HEPTANE'>HP6</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=R16:HEXADECANE'>R16</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4QL:2,4,6-TRIS(IODANYL)-5-(OCTANOYLAMINO)BENZENE-1,3-DICARBOXYLIC+ACID'>4QL</scene>, <scene name='pdbligand=D10:DECANE'>D10</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=DD9:NONANE'>DD9</scene>, <scene name='pdbligand=HP6:HEPTANE'>HP6</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=R16:HEXADECANE'>R16</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5b35\|5b35]]~~</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=5b34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b34 OCA], [https://pdbe.org/5b34 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b34 RCSB], [https://www.ebi.ac.uk/pdbsum/5b34 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b34 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=5b34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b34 OCA], [~~http~~://pdbe.org/5b34 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5b34 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5b34 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5b34 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA]] Light-driven proton pump.	+	[https://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA] Light-driven proton pump.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 28:		Line 27:
	[[Category: Halobacterium salinarum]]		[[Category: Halobacterium salinarum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Mizohata, E]]	+	[[Category: Mizohata E]]
-	[[Category: Nakane, T]]	+	[[Category: Nakane T]]
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Proton pump]]~~	+
-	~~[[Category: Proton transport]]~~	+
-	~~[[Category: Retinal]]~~	+
-	~~[[Category: Sad]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 08:45, 11 March 2020

OCA — Wed, 11 Mar 2020 08:45:38 GMT

←Older revision		Revision as of 08:45, 11 March 2020
Line 1:		Line 1:

	==Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles in Complex with Iodine-labeled Detergent HAD13a Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA==		==Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles in Complex with Iodine-labeled Detergent HAD13a Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA==
-	<StructureSection load='5b34' size='340' side='right' caption='[[5b34]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5b34' size='340' side='right'caption='[[5b34]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5b34]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B34 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B34 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5b34]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B34 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B34 FirstGlance]. <br>
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5b34" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5b34" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Bacteriorhodopsin 3D structures\|Bacteriorhodopsin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Halobacterium salinarum]]		[[Category: Halobacterium salinarum]]
		+	[[Category: Large Structures]]
	[[Category: Mizohata, E]]		[[Category: Mizohata, E]]
	[[Category: Nakane, T]]		[[Category: Nakane, T]]

OCA at 19:43, 9 December 2016

OCA — Fri, 09 Dec 2016 19:43:45 GMT

←Older revision		Revision as of 19:43, 9 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5b34 is ~~ON HOLD until Paper~~ Publication	+	==Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles in Complex with Iodine-labeled Detergent HAD13a Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA==
		+	<StructureSection load='5b34' size='340' side='right' caption='[[5b34]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5b34]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B34 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B34 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4QL:2,4,6-TRIS(IODANYL)-5-(OCTANOYLAMINO)BENZENE-1,3-DICARBOXYLIC+ACID'>4QL</scene>, <scene name='pdbligand=D10:DECANE'>D10</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=DD9:NONANE'>DD9</scene>, <scene name='pdbligand=HP6:HEPTANE'>HP6</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=R16:HEXADECANE'>R16</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5b35\|5b35]]</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=5b34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b34 OCA], [http://pdbe.org/5b34 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b34 RCSB], [http://www.ebi.ac.uk/pdbsum/5b34 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b34 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA]] Light-driven proton pump.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The 3D structure determination of biological macromolecules by X-ray crystallography suffers from a phase problem: to perform Fourier transformation to calculate real space density maps, both intensities and phases of structure factors are necessary; however, measured diffraction patterns give only intensities. Although serial femtosecond crystallography (SFX) using X-ray free electron lasers (XFELs) has been steadily developed since 2009, experimental phasing still remains challenging. Here, using 7.0-keV (1.771 A) X-ray pulses from the SPring-8 Angstrom Compact Free Electron Laser (SACLA), iodine single-wavelength anomalous diffraction (SAD), single isomorphous replacement (SIR), and single isomorphous replacement with anomalous scattering (SIRAS) phasing were performed in an SFX regime for a model membrane protein bacteriorhodopsin (bR). The crystals grown in bicelles were derivatized with an iodine-labeled detergent heavy-atom additive 13a (HAD13a), which contains the magic triangle, I3C head group with three iodine atoms. The alkyl tail was essential for binding of the detergent to the surface of bR. Strong anomalous and isomorphous difference signals from HAD13a enabled successful phasing using reflections up to 2.1-A resolution from only 3,000 and 4,000 indexed images from native and derivative crystals, respectively. When more images were merged, structure solution was possible with data truncated at 3.3-A resolution, which is the lowest resolution among the reported cases of SFX phasing. Moreover, preliminary SFX experiment showed that HAD13a successfully derivatized the G protein-coupled A2a adenosine receptor crystallized in lipidic cubic phases. These results pave the way for de novo structure determination of membrane proteins, which often diffract poorly, even with the brightest XFEL beams.

-	~~Authors~~:	+	Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent.,Nakane T, Hanashima S, Suzuki M, Saiki H, Hayashi T, Kakinouchi K, Sugiyama S, Kawatake S, Matsuoka S, Matsumori N, Nango E, Kobayashi J, Shimamura T, Kimura K, Mori C, Kunishima N, Sugahara M, Takakyu Y, Inoue S, Masuda T, Hosaka T, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Inoue T, Nureki O, Iwata S, Murata M, Mizohata E Proc Natl Acad Sci U S A. 2016 Nov 15;113(46):13039-13044. Epub 2016 Oct 31. PMID:27799539<ref>PMID:27799539</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5b34" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Halobacterium salinarum]]
		+	[[Category: Mizohata, E]]
		+	[[Category: Nakane, T]]
		+	[[Category: Membrane protein]]
		+	[[Category: Proton pump]]
		+	[[Category: Proton transport]]
		+	[[Category: Retinal]]
		+	[[Category: Sad]]
		+	[[Category: Transport protein]]

OCA at 07:03, 21 September 2016

OCA — Wed, 21 Sep 2016 07:03:43 GMT

←Older revision		Revision as of 07:03, 21 September 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5b34 is ON HOLD	+	The entry 5b34 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 11:05, 15 May 2016

OCA — Sun, 15 May 2016 11:05:47 GMT

←Older revision		Revision as of 11:05, 15 May 2016
Line 3:		Line 3:
	The entry 5b34 is ON HOLD		The entry 5b34 is ON HOLD

-	Authors: ~~Mizohata, E., Nakane, T.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Mizohata, E]]
-	[[Category: Nakane, T]]

OCA: Protected "5b34" [edit=sysop:move=sysop]

OCA — Sat, 20 Feb 2016 21:12:51 GMT

Protected "5b34" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:12, 20 February 2016

OCA: New page: '''Unreleased structure''' The entry 5b34 is ON HOLD Authors: Mizohata, E., Nakane, T. Description: Category: Unreleased Structures Category: Mizohata, E [[Category: Nakane, T...

OCA — Sat, 20 Feb 2016 21:12:49 GMT

New page: '''Unreleased structure''' The entry 5b34 is ON HOLD Authors: Mizohata, E., Nakane, T. Description: Category: Unreleased Structures Category: Mizohata, E [[Category: Nakane, T...

New page

'''Unreleased structure'''

The entry 5b34 is ON HOLD

Authors: Mizohata, E., Nakane, T.

Description:
[[Category: Unreleased Structures]]
[[Category: Mizohata, E]]
[[Category: Nakane, T]]