1nkz - Revision history

OCA at 13:27, 13 March 2024

OCA — Wed, 13 Mar 2024 13:27:57 GMT

←Older revision		Revision as of 13:27, 13 March 2024
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nkz ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nkz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The structure at 100K of integral membrane light-harvesting complex II (LH2) from Rhodopseudomonas acidophila strain 10050 has been refined to 2.0A resolution. The electron density has been significantly improved, compared to the 2.5A resolution map, by high resolution data, cryo-cooling and translation, libration, screw (TLS) refinement. The electron density reveals a second carotenoid molecule, the last five C-terminal residues of the alpha-chain and a carboxy modified alpha-Met1 which forms the ligand of the B800 bacteriochlorophyll. TLS refinement has enabled the characterisation of displacements between molecules in the complex. B850 bacteriochlorophyll molecules are arranged in a ring of 18 pigments composed of nine approximate dimers. These pigments are strongly coupled and at their equilibrium positions the excited state dipole interaction energies, within and between dimers, are approximately 370cm(-1) and 280cm(-1), respectively. This difference in coupling energy is similar in magnitude to changes in interaction energies arising from the pigment displacements described by TLS tensors. The displacements appear to be non-random in nature and appear to be designed to optimise the modulation of pigment energy interactions. This is the first time that LH2 pigment displacements have been quantified experimentally. The calculated energy changes indicate that there may be significant contributions to inter-pigment energy interactions from molecular displacements and these may be of importance to photosynthetic energy transfer.
-
-	The structure and thermal motion of the B800-850 LH2 complex from Rps.acidophila at 2.0A resolution and 100K: new structural features and functionally relevant motions.,Papiz MZ, Prince SM, Howard T, Cogdell RJ, Isaacs NW J Mol Biol. 2003 Mar 7;326(5):1523-38. PMID:12595263<ref>PMID:12595263</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1nkz" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 09:21, 16 August 2023

OCA — Wed, 16 Aug 2023 09:21:36 GMT

←Older revision		Revision as of 09:21, 16 August 2023
Line 3:		Line 3:
	<StructureSection load='1nkz' size='340' side='right'caption='[[1nkz]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1nkz' size='340' side='right'caption='[[1nkz]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nkz]] is a 6 chain structure with sequence from [~~http://en.wikipedia.org/wiki/Atcc_25092 Atcc 25092] and [http~~://en.wikipedia.org/wiki/Rhodoblastus_acidophilus Rhodoblastus acidophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1NKZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nkz]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodoblastus_acidophilus Rhodoblastus acidophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NKZ FirstGlance]. <br>
-	</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=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=~~RG1~~:~~RHODOPIN+B~~-~~D-GLUCOSIDE~~'>~~RG1~~</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]] 2Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~CXM~~:N-~~CARBOXYMETHIONINE~~'>~~CXM~~</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=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene>, <scene name='pdbligand=RG1:RHODOPIN+B-D-GLUCOSIDE'>RG1</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kzu\|1kzu]]~~</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=1nkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkz OCA], [https://pdbe.org/1nkz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nkz RCSB], [https://www.ebi.ac.uk/pdbsum/1nkz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nkz ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1nkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkz OCA], [~~http~~://pdbe.org/1nkz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1nkz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1nkz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1nkz ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/LHA4_RHOAC LHA4_RHOAC~~]] Antenna complexes are light-harvesting systems, which transfer the excitation energy to the reaction centers. [[http://www.uniprot.org/uniprot/LHB5_RHOAC LHB5_RHOAC]~~] Antenna complexes are light-harvesting systems, which transfer the excitation energy to the reaction centers.	+	[https://www.uniprot.org/uniprot/LHA4_RHOAC LHA4_RHOAC] Antenna complexes are light-harvesting systems, which transfer the excitation energy to the reaction centers.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 25092]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Rhodoblastus acidophilus]]		[[Category: Rhodoblastus acidophilus]]
-	[[Category: Cogdell~~, R J~~]]	+	[[Category: Cogdell RJ]]
-	[[Category: Howard, T]]	+	[[Category: Howard T]]
-	[[Category: Isaacs~~, N W~~]]	+	[[Category: Isaacs NW]]
-	[[Category: Papiz~~, M Z~~]]	+	[[Category: Papiz MZ]]
-	[[Category: Prince~~, S M]]~~	+	[[Category: Prince SM]]
-	~~[[Category: Bacteriochlorophyll some]]~~	+
-	~~[[Category: Light harvesting complex ii]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Photosynthesis]]~~	+
-	~~[[Category: Rhodopin glucoside]]~~	+
-	~~[[Category: Trans-membrane helice~~]]	+

OCA at 10:37, 16 September 2020

OCA — Wed, 16 Sep 2020 10:37:42 GMT

←Older revision		Revision as of 10:37, 16 September 2020
Line 1:		Line 1:

	==Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution==		==Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution==
-	<StructureSection load='1nkz' size='340' side='right' caption='[[1nkz]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1nkz' size='340' side='right'caption='[[1nkz]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nkz]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25092 Atcc 25092] and [http://en.wikipedia.org/wiki/Rhodoblastus_acidophilus Rhodoblastus acidophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKZ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1NKZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nkz]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25092 Atcc 25092] and [http://en.wikipedia.org/wiki/Rhodoblastus_acidophilus Rhodoblastus acidophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1NKZ 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=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=RG1:RHODOPIN+B-D-GLUCOSIDE'>RG1</scene></td></tr>	+	</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=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=RG1:RHODOPIN+B-D-GLUCOSIDE'>RG1</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kzu\|1kzu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kzu\|1kzu]]</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=1nkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkz OCA], [http://pdbe.org/1nkz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nkz RCSB], [http://www.ebi.ac.uk/pdbsum/1nkz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nkz ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1nkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkz OCA], [http://pdbe.org/1nkz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nkz RCSB], [http://www.ebi.ac.uk/pdbsum/1nkz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nkz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 25092]]		[[Category: Atcc 25092]]
		+	[[Category: Large Structures]]
	[[Category: Rhodoblastus acidophilus]]		[[Category: Rhodoblastus acidophilus]]
	[[Category: Cogdell, R J]]		[[Category: Cogdell, R J]]

OCA at 07:47, 12 December 2018

OCA — Wed, 12 Dec 2018 07:47:45 GMT

←Older revision		Revision as of 07:47, 12 December 2018
Line 3:		Line 3:
	<StructureSection load='1nkz' size='340' side='right' caption='[[1nkz]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1nkz' size='340' side='right' caption='[[1nkz]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nkz]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Rhodoblastus_acidophilus Rhodoblastus acidophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NKZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nkz]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25092 Atcc 25092] and [http://en.wikipedia.org/wiki/Rhodoblastus_acidophilus Rhodoblastus acidophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NKZ 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=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=RG1:RHODOPIN+B-D-GLUCOSIDE'>RG1</scene></td></tr>		</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=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=RG1:RHODOPIN+B-D-GLUCOSIDE'>RG1</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nk/1nkz_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nk/1nkz_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 34:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 25092]]
	[[Category: Rhodoblastus acidophilus]]		[[Category: Rhodoblastus acidophilus]]
	[[Category: Cogdell, R J]]		[[Category: Cogdell, R J]]

OCA at 11:05, 1 February 2017

OCA — Wed, 01 Feb 2017 11:05:07 GMT

←Older revision		Revision as of 11:05, 1 February 2017
Line 3:		Line 3:
	<StructureSection load='1nkz' size='340' side='right' caption='[[1nkz]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1nkz' size='340' side='right' caption='[[1nkz]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nkz]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Atcc_25092 Atcc 25092~~] and [http://en.wikipedia.org/wiki/Rhodoblastus_acidophilus Rhodoblastus acidophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NKZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nkz]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Rhodoblastus_acidophilus Rhodoblastus acidophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NKZ 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=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=RG1:RHODOPIN+B-D-GLUCOSIDE'>RG1</scene></td></tr>		</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=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=RG1:RHODOPIN+B-D-GLUCOSIDE'>RG1</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kzu\|1kzu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kzu\|1kzu]]</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=1nkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkz OCA], [http://pdbe.org/1nkz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nkz RCSB], [http://www.ebi.ac.uk/pdbsum/1nkz 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=1nkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkz OCA], [http://pdbe.org/1nkz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nkz RCSB], [http://www.ebi.ac.uk/pdbsum/1nkz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nkz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 34:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 25092]]
	[[Category: Rhodoblastus acidophilus]]		[[Category: Rhodoblastus acidophilus]]
	[[Category: Cogdell, R J]]		[[Category: Cogdell, R J]]

OCA at 16:22, 10 May 2016

OCA — Tue, 10 May 2016 16:22:18 GMT

OCA at 10:34, 11 September 2015

OCA — Fri, 11 Sep 2015 10:34:13 GMT

←Older revision		Revision as of 10:34, 11 September 2015
Line 6:		Line 6:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kzu\|1kzu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kzu\|1kzu]]</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=1nkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nkz RCSB], [http://www.ebi.ac.uk/pdbsum/1nkz 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=1nkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkz OCA], [http://pdbe.org/1nkz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nkz RCSB], [http://www.ebi.ac.uk/pdbsum/1nkz PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1nkz" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:16, 25 December 2014

OCA — Thu, 25 Dec 2014 15:16:43 GMT

←Older revision		Revision as of 15:16, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1nkz]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25092 Atcc 25092] and [http://en.wikipedia.org/wiki/Rhodoblastus_acidophilus Rhodoblastus acidophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NKZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1nkz]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25092 Atcc 25092] and [http://en.wikipedia.org/wiki/Rhodoblastus_acidophilus Rhodoblastus acidophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NKZ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=RG1:RHODOPIN+GLUCOSIDE'>RG1</scene><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=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=RG1:RHODOPIN+GLUCOSIDE'>RG1</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kzu\|1kzu]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kzu\|1kzu]]</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=1nkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nkz RCSB], [http://www.ebi.ac.uk/pdbsum/1nkz 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=1nkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nkz RCSB], [http://www.ebi.ac.uk/pdbsum/1nkz PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LHA4_RHOAC LHA4_RHOAC]] Antenna complexes are light-harvesting systems, which transfer the excitation energy to the reaction centers. [[http://www.uniprot.org/uniprot/LHB5_RHOAC LHB5_RHOAC]] Antenna complexes are light-harvesting systems, which transfer the excitation energy to the reaction centers.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	[[Category: Atcc 25092]]		[[Category: Atcc 25092]]
	[[Category: Rhodoblastus acidophilus]]		[[Category: Rhodoblastus acidophilus]]
-	[[Category: Cogdell, R J.]]	+	[[Category: Cogdell, R J]]
	[[Category: Howard, T]]		[[Category: Howard, T]]
-	[[Category: Isaacs, N W.]]	+	[[Category: Isaacs, N W]]
-	[[Category: Papiz, M Z.]]	+	[[Category: Papiz, M Z]]
-	[[Category: Prince, S M.]]	+	[[Category: Prince, S M]]
	[[Category: Bacteriochlorophyll some]]		[[Category: Bacteriochlorophyll some]]
	[[Category: Light harvesting complex ii]]		[[Category: Light harvesting complex ii]]

OCA at 08:25, 3 October 2014

OCA — Fri, 03 Oct 2014 08:25:39 GMT

←Older revision		Revision as of 08:25, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1nkz\| PDB=1nkz \| SCENE= }}~~	+	==Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution==
-	===Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution===	+	<StructureSection load='1nkz' size='340' side='right' caption='[[1nkz]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~{{ABSTRACT_PUBMED_12595263}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1nkz]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25092 Atcc 25092] and [http://en.wikipedia.org/wiki/Rhodoblastus_acidophilus Rhodoblastus acidophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NKZ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=RG1:RHODOPIN+GLUCOSIDE'>RG1</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kzu\|1kzu]]</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=1nkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nkz RCSB], [http://www.ebi.ac.uk/pdbsum/1nkz PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nk/1nkz_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The structure at 100K of integral membrane light-harvesting complex II (LH2) from Rhodopseudomonas acidophila strain 10050 has been refined to 2.0A resolution. The electron density has been significantly improved, compared to the 2.5A resolution map, by high resolution data, cryo-cooling and translation, libration, screw (TLS) refinement. The electron density reveals a second carotenoid molecule, the last five C-terminal residues of the alpha-chain and a carboxy modified alpha-Met1 which forms the ligand of the B800 bacteriochlorophyll. TLS refinement has enabled the characterisation of displacements between molecules in the complex. B850 bacteriochlorophyll molecules are arranged in a ring of 18 pigments composed of nine approximate dimers. These pigments are strongly coupled and at their equilibrium positions the excited state dipole interaction energies, within and between dimers, are approximately 370cm(-1) and 280cm(-1), respectively. This difference in coupling energy is similar in magnitude to changes in interaction energies arising from the pigment displacements described by TLS tensors. The displacements appear to be non-random in nature and appear to be designed to optimise the modulation of pigment energy interactions. This is the first time that LH2 pigment displacements have been quantified experimentally. The calculated energy changes indicate that there may be significant contributions to inter-pigment energy interactions from molecular displacements and these may be of importance to photosynthetic energy transfer.

-	~~==Function==~~	+	The structure and thermal motion of the B800-850 LH2 complex from Rps.acidophila at 2.0A resolution and 100K: new structural features and functionally relevant motions.,Papiz MZ, Prince SM, Howard T, Cogdell RJ, Isaacs NW J Mol Biol. 2003 Mar 7;326(5):1523-38. PMID:12595263<ref>PMID:12595263</ref>
-	~~[[http~~:~~//www~~.~~uniprot~~.~~org/uniprot/LHA4_RHOAC LHA4_RHOAC]] Antenna complexes are light~~-~~harvesting systems, which transfer the excitation energy to the reaction centers~~. ~~[[http~~:/~~/www.uniprot.org/uniprot/LHB5_RHOAC LHB5_RHOAC]] Antenna complexes are light-harvesting systems, which transfer the excitation energy to the reaction centers.~~	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[1nkz]] is~~ a ~~6 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Atcc_25092 Atcc 25092] and [http://en~~.~~wikipedia.org~~/~~wiki/Rhodoblastus_acidophilus Rhodoblastus acidophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKZ OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:012595263</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Atcc 25092]]		[[Category: Atcc 25092]]
	[[Category: Rhodoblastus acidophilus]]		[[Category: Rhodoblastus acidophilus]]

OCA at 08:00, 16 April 2014

OCA — Wed, 16 Apr 2014 08:00:31 GMT

←Older revision		Revision as of 08:00, 16 April 2014
Line 1:		Line 1:
-	[[Image:1nkz.png\|left\|200px]]
-
	{{STRUCTURE_1nkz\| PDB=1nkz \| SCENE= }}		{{STRUCTURE_1nkz\| PDB=1nkz \| SCENE= }}
-
	===Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution===		===Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution===
		+	{{ABSTRACT_PUBMED_12595263}}

-	~~{{ABSTRACT_PUBMED_12595263}}~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/LHA4_RHOAC LHA4_RHOAC]] Antenna complexes are light-harvesting systems, which transfer the excitation energy to the reaction centers. [[http://www.uniprot.org/uniprot/LHB5_RHOAC LHB5_RHOAC]] Antenna complexes are light-harvesting systems, which transfer the excitation energy to the reaction centers.

	==About this Structure==		==About this Structure==
-	[[1nkz]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodoblastus_acidophilus Rhodoblastus acidophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKZ OCA].	+	[[1nkz]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25092 Atcc 25092] and [http://en.wikipedia.org/wiki/Rhodoblastus_acidophilus Rhodoblastus acidophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKZ OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:012595263</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012595263</ref><references group="xtra"/><references/>
		+	[[Category: Atcc 25092]]
	[[Category: Rhodoblastus acidophilus]]		[[Category: Rhodoblastus acidophilus]]
	[[Category: Cogdell, R J.]]		[[Category: Cogdell, R J.]]

←Older revision		Revision as of 16:22, 10 May 2016
Line 1:		Line 1:
		+
	==Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution==		==Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution==
	<StructureSection load='1nkz' size='340' side='right' caption='[[1nkz]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1nkz' size='340' side='right' caption='[[1nkz]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1nkz]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25092 Atcc 25092] and [http://en.wikipedia.org/wiki/Rhodoblastus_acidophilus Rhodoblastus acidophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NKZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1nkz]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25092 Atcc 25092] and [http://en.wikipedia.org/wiki/Rhodoblastus_acidophilus Rhodoblastus acidophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NKZ 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=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=RG1:RHODOPIN+GLUCOSIDE'>RG1</scene></td></tr>	+	</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=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=RG1:RHODOPIN+B-D-GLUCOSIDE'>RG1</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kzu\|1kzu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kzu\|1kzu]]</td></tr>
Line 18:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nkz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">