5m7j - Revision history

OCA at 18:28, 1 November 2023

2023-11-01T18:28:32Z

←Older revision		Revision as of 18:28, 1 November 2023
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	<StructureSection load='5m7j' size='340' side='right'caption='[[5m7j]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='5m7j' size='340' side='right'caption='[[5m7j]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5m7j]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Blastochloris_viridis Blastochloris viridis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M7J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5M7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5m7j]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Blastochloris_viridis Blastochloris viridis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5M7J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BPB:BACTERIOPHEOPHYTIN+B'>BPB</scene>, <scene name='pdbligand=DGA:DIACYL+GLYCEROL'>DGA</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=MPG:[(Z)-OCTADEC-9-ENYL]+(2R)-2,3-BIS(OXIDANYL)PROPANOATE'>MPG</scene>, <scene name='pdbligand=MQ7:MENAQUINONE-7'>MQ7</scene>, <scene name='pdbligand=NS5:15-CIS-1,2-DIHYDRONEUROSPORENE'>NS5</scene>, <scene name='pdbligand=OTP:(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL+TRIHYDROGEN+DIPHOSPHATE'>OTP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4~~</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]] 3.5Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME~~</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BPB:BACTERIOPHEOPHYTIN+B'>BPB</scene>, <scene name='pdbligand=DGA:DIACYL+GLYCEROL'>DGA</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=MPG:[(Z)-OCTADEC-9-ENYL]+(2R)-2,3-BIS(OXIDANYL)PROPANOATE'>MPG</scene>, <scene name='pdbligand=MQ7:MENAQUINONE-7'>MQ7</scene>, <scene name='pdbligand=NS5:15-CIS-1,2-DIHYDRONEUROSPORENE'>NS5</scene>, <scene name='pdbligand=OTP:(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL+TRIHYDROGEN+DIPHOSPHATE'>OTP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=5m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m7j OCA], [~~http~~://pdbe.org/5m7j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5m7j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5m7j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5m7j 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=5m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m7j OCA], [https://pdbe.org/5m7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5m7j RCSB], [https://www.ebi.ac.uk/pdbsum/5m7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5m7j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/RCEH_BLAVI RCEH_BLAVI]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis. [[http://www.uniprot.org/uniprot/CYCR_BLAVI CYCR_BLAVI]] The reaction center of purple bacteria contains a tightly bound cytochrome molecule which re-reduces the photo oxidized primary electron donor.<ref>PMID:10736158</ref> [[http://www.uniprot.org/uniprot/RCEM_BLAVI RCEM_BLAVI]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis. [[http://www.uniprot.org/uniprot/RCEL_BLAVI RCEL_BLAVI]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis.	+	[https://www.uniprot.org/uniprot/CYCR_BLAVI CYCR_BLAVI] The reaction center of purple bacteria contains a tightly bound cytochrome molecule which re-reduces the photo oxidized primary electron donor.<ref>PMID:10736158</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	[[Category: Blastochloris viridis]]		[[Category: Blastochloris viridis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dunevall, E]]	+	[[Category: Dunevall E]]
-	[[Category: Johansson, L]]	+	[[Category: Johansson L]]
-	[[Category: Katona, G]]	+	[[Category: Katona G]]
-	[[Category: Neutze, R]]	+	[[Category: Neutze R]]
-	[[Category: Sharma~~, A S~~]]	+	[[Category: Sharma AS]]
-	[[Category: Wahlgren~~, W Y]]~~	+	[[Category: Wahlgren WY]]
-	~~[[Category: Photosynthesis]]~~	+
-	~~[[Category: Photosynthetic]]~~	+
-	~~[[Category: Reaction center~~]]	+

OCA at 06:34, 16 October 2019

2019-10-16T06:34:19Z

←Older revision		Revision as of 06:34, 16 October 2019
Line 1:		Line 1:

	==Blastochloris viridis photosynthetic reaction center structure using best crystal approach==		==Blastochloris viridis photosynthetic reaction center structure using best crystal approach==
-	<StructureSection load='5m7j' size='340' side='right' caption='[[5m7j]], [[Resolution\|resolution]] 3.50Å' scene=''>	+	<StructureSection load='5m7j' size='340' side='right'caption='[[5m7j]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5m7j]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Blastochloris_viridis Blastochloris viridis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5M7J FirstGlance]. <br>		<table><tr><td colspan='2'>[[5m7j]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Blastochloris_viridis Blastochloris viridis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5M7J FirstGlance]. <br>
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Blastochloris viridis]]		[[Category: Blastochloris viridis]]
		+	[[Category: Large Structures]]
	[[Category: Dunevall, E]]		[[Category: Dunevall, E]]
	[[Category: Johansson, L]]		[[Category: Johansson, L]]

OCA at 06:53, 9 March 2017

2017-03-09T06:53:25Z

←Older revision		Revision as of 06:53, 9 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5m7j is ~~ON HOLD~~	+	==Blastochloris viridis photosynthetic reaction center structure using best crystal approach==
		+	<StructureSection load='5m7j' size='340' side='right' caption='[[5m7j]], [[Resolution\|resolution]] 3.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5m7j]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Blastochloris_viridis Blastochloris viridis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5M7J FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BPB:BACTERIOPHEOPHYTIN+B'>BPB</scene>, <scene name='pdbligand=DGA:DIACYL+GLYCEROL'>DGA</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=MPG:[(Z)-OCTADEC-9-ENYL]+(2R)-2,3-BIS(OXIDANYL)PROPANOATE'>MPG</scene>, <scene name='pdbligand=MQ7:MENAQUINONE-7'>MQ7</scene>, <scene name='pdbligand=NS5:15-CIS-1,2-DIHYDRONEUROSPORENE'>NS5</scene>, <scene name='pdbligand=OTP:(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL+TRIHYDROGEN+DIPHOSPHATE'>OTP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</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=5m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m7j OCA], [http://pdbe.org/5m7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m7j RCSB], [http://www.ebi.ac.uk/pdbsum/5m7j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m7j ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RCEH_BLAVI RCEH_BLAVI]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis. [[http://www.uniprot.org/uniprot/CYCR_BLAVI CYCR_BLAVI]] The reaction center of purple bacteria contains a tightly bound cytochrome molecule which re-reduces the photo oxidized primary electron donor.<ref>PMID:10736158</ref> [[http://www.uniprot.org/uniprot/RCEM_BLAVI RCEM_BLAVI]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis. [[http://www.uniprot.org/uniprot/RCEL_BLAVI RCEL_BLAVI]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Serial crystallography is an increasingly important approach to protein crystallography that exploits both X-ray free-electron laser (XFEL) and synchrotron radiation. Serial crystallography recovers complete X-ray diffraction data by processing and merging diffraction images from thousands of randomly oriented non-uniform microcrystals, of which all observations are partial Bragg reflections. Random fluctuations in the XFEL pulse energy spectrum, variations in the size and shape of microcrystals, integrating over millions of weak partial observations and instabilities in the XFEL beam position lead to new types of experimental errors. The quality of Bragg intensity estimates deriving from serial crystallography is therefore contingent upon assumptions made while modeling these data. Here it is observed that serial femtosecond crystallography (SFX) Bragg reflections do not follow a unimodal Gaussian distribution and it is recommended that an idealized assumption of single Gaussian peak profiles be relaxed to incorporate apparent asymmetries when processing SFX data. The phenomenon is illustrated by re-analyzing data collected from microcrystals of the Blastochloris viridis photosynthetic reaction center and comparing these intensity observations with conventional synchrotron data. The results show that skewness in the SFX observations captures the essence of the Wilson plot and an empirical treatment is suggested that can help to separate the diffraction Bragg intensity from the background.

-	~~Authors: Sharma~~, A~~.S.~~, Johansson, L., Dunevall, E., Wahlgren~~, W.Y.~~, Neutze, R., Katona, G.	+	Asymmetry in serial femtosecond crystallography data.,Sharma A, Johansson L, Dunevall E, Wahlgren WY, Neutze R, Katona G Acta Crystallogr A Found Adv. 2017 Mar 1;73(Pt 2):93-101. doi:, 10.1107/S2053273316018696. Epub 2017 Jan 30. PMID:28248658<ref>PMID:28248658</ref>

-	~~Description~~: ~~Blastochloris viridis photosynthetic reaction center structure using best crystal approach~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5m7j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Blastochloris viridis]]
	[[Category: Dunevall, E]]		[[Category: Dunevall, E]]
-	[[Category: Sharma, A.S]]
-	[[Category: Katona, G]]
-	[[Category: Wahlgren, W.Y]]
	[[Category: Johansson, L]]		[[Category: Johansson, L]]
		+	[[Category: Katona, G]]
	[[Category: Neutze, R]]		[[Category: Neutze, R]]
		+	[[Category: Sharma, A S]]
		+	[[Category: Wahlgren, W Y]]
		+	[[Category: Photosynthesis]]
		+	[[Category: Photosynthetic]]
		+	[[Category: Reaction center]]

OCA: Protected "5m7j" [edit=sysop:move=sysop]

2016-11-02T16:06:54Z

Protected "5m7j" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:06, 2 November 2016

OCA: New page: '''Unreleased structure''' The entry 5m7j is ON HOLD Authors: Sharma, A.S., Johansson, L., Dunevall, E., Wahlgren, W.Y., Neutze, R., Katona, G. Description: Blastochloris viridis photo...

2016-11-02T16:06:52Z

New page: '''Unreleased structure''' The entry 5m7j is ON HOLD Authors: Sharma, A.S., Johansson, L., Dunevall, E., Wahlgren, W.Y., Neutze, R., Katona, G. Description: Blastochloris viridis photo...

New page

'''Unreleased structure'''

The entry 5m7j is ON HOLD

Authors: Sharma, A.S., Johansson, L., Dunevall, E., Wahlgren, W.Y., Neutze, R., Katona, G.

Description: Blastochloris viridis photosynthetic reaction center structure using best crystal approach
[[Category: Unreleased Structures]]
[[Category: Dunevall, E]]
[[Category: Sharma, A.S]]
[[Category: Katona, G]]
[[Category: Wahlgren, W.Y]]
[[Category: Johansson, L]]
[[Category: Neutze, R]]