1ztu - Revision history

OCA at 08:13, 15 May 2024

OCA — Wed, 15 May 2024 08:13:04 GMT

←Older revision		Revision as of 08:13, 15 May 2024
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	<StructureSection load='1ztu' size='340' side='right'caption='[[1ztu]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1ztu' size='340' side='right'caption='[[1ztu]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ztu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus~~ radiodurans~~" raj et al. 1960~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZTU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZTU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ztu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZTU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZTU FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</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]] 2.5Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">bphP ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])~~</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=1ztu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ztu OCA], [https://pdbe.org/1ztu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ztu RCSB], [https://www.ebi.ac.uk/pdbsum/1ztu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ztu 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=1ztu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ztu OCA], [https://pdbe.org/1ztu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ztu RCSB], [https://www.ebi.ac.uk/pdbsum/1ztu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ztu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/BPHY_DEIRA BPHY_DEIRA]] Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region. Has also a slight blue shift for the far-red maximum. Could also absorb green light. May participate in regulating pigment synthesis like the carotenoid deinoxanthin which could protect the bacterium from intense visible light.	+	[https://www.uniprot.org/uniprot/BPHY_DEIRA BPHY_DEIRA] Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region. Has also a slight blue shift for the far-red maximum. Could also absorb green light. May participate in regulating pigment synthesis like the carotenoid deinoxanthin which could protect the bacterium from intense visible light.
	== 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: ~~Micrococcus~~ radiodurans ~~raj et al. 1960~~]]	+	[[Category: Deinococcus radiodurans]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brunzelle~~, J S~~]]	+	[[Category: Brunzelle JS]]
-	[[Category: Forest~~, K T~~]]	+	[[Category: Forest KT]]
-	[[Category: Vierstra~~, R D~~]]	+	[[Category: Vierstra RD]]
-	[[Category: Wagner~~, J R]]~~	+	[[Category: Wagner JR]]
-	~~[[Category: Bacteriophytochrome]]~~	+
-	~~[[Category: Biliverdin ix]]~~	+
-	~~[[Category: Chromophore]]~~	+
-	~~[[Category: Gaf]]~~	+
-	~~[[Category: Knot]]~~	+
-	~~[[Category: Pa]]~~	+
-	~~[[Category: Phytochrome]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:17, 27 January 2021

OCA — Wed, 27 Jan 2021 08:17:06 GMT

←Older revision		Revision as of 08:17, 27 January 2021
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	==Structure of the chromophore binding domain of bacterial phytochrome==		==Structure of the chromophore binding domain of bacterial phytochrome==
-	<StructureSection load='1ztu' size='340' side='right' caption='[[1ztu]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='1ztu' size='340' side='right'caption='[[1ztu]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ztu]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZTU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1ZTU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ztu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZTU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZTU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</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=1ztu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ztu OCA], [~~http~~://pdbe.org/1ztu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ztu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ztu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ztu 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=1ztu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ztu OCA], [https://pdbe.org/1ztu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ztu RCSB], [https://www.ebi.ac.uk/pdbsum/1ztu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ztu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/BPHY_DEIRA BPHY_DEIRA]] Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region. Has also a slight blue shift for the far-red maximum. Could also absorb green light. May participate in regulating pigment synthesis like the carotenoid deinoxanthin which could protect the bacterium from intense visible light.	+	[[https://www.uniprot.org/uniprot/BPHY_DEIRA BPHY_DEIRA]] Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region. Has also a slight blue shift for the far-red maximum. Could also absorb green light. May participate in regulating pigment synthesis like the carotenoid deinoxanthin which could protect the bacterium from intense visible light.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zt/1ztu_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zt/1ztu_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 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Micrococcus radiodurans raj et al. 1960]]		[[Category: Micrococcus radiodurans raj et al. 1960]]
		+	[[Category: Large Structures]]
	[[Category: Brunzelle, J S]]		[[Category: Brunzelle, J S]]
	[[Category: Forest, K T]]		[[Category: Forest, K T]]

OCA at 11:07, 12 October 2017

OCA — Thu, 12 Oct 2017 11:07:53 GMT

←Older revision		Revision as of 11:07, 12 October 2017
Line 1:		Line 1:
		+
	==Structure of the chromophore binding domain of bacterial phytochrome==		==Structure of the chromophore binding domain of bacterial phytochrome==
	<StructureSection load='1ztu' size='340' side='right' caption='[[1ztu]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1ztu' size='340' side='right' caption='[[1ztu]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</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=1ztu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ztu OCA], [http://pdbe.org/1ztu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ztu RCSB], [http://www.ebi.ac.uk/pdbsum/1ztu 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=1ztu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ztu OCA], [http://pdbe.org/1ztu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ztu RCSB], [http://www.ebi.ac.uk/pdbsum/1ztu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ztu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 22:16, 9 February 2016

OCA — Tue, 09 Feb 2016 22:16:39 GMT

←Older revision		Revision as of 22:16, 9 February 2016
Line 18:		Line 18:
	<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=1ztu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:33, 11 September 2015

OCA — Fri, 11 Sep 2015 02:33:59 GMT

←Older revision		Revision as of 02:33, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1ztu' size='340' side='right' caption='[[1ztu]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1ztu' size='340' side='right' caption='[[1ztu]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ztu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Deinococcus_radiodurans Deinococcus~~ radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZTU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZTU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ztu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZTU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZTU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 ~~Deinococcus~~ radiodurans])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</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=1ztu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ztu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ztu RCSB], [http://www.ebi.ac.uk/pdbsum/1ztu 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=1ztu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ztu OCA], [http://pdbe.org/1ztu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ztu RCSB], [http://www.ebi.ac.uk/pdbsum/1ztu 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 1ztu" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Deinococcus~~ radiodurans]]	+	[[Category: Micrococcus radiodurans raj et al. 1960]]
	[[Category: Brunzelle, J S]]		[[Category: Brunzelle, J S]]
	[[Category: Forest, K T]]		[[Category: Forest, K T]]

OCA at 09:53, 25 December 2014

OCA — Thu, 25 Dec 2014 09:53:59 GMT

←Older revision		Revision as of 09:53, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ztu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZTU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZTU FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ztu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZTU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZTU FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 Deinococcus radiodurans])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 Deinococcus radiodurans])</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=1ztu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ztu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ztu RCSB], [http://www.ebi.ac.uk/pdbsum/1ztu 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=1ztu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ztu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ztu RCSB], [http://www.ebi.ac.uk/pdbsum/1ztu PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BPHY_DEIRA BPHY_DEIRA]] Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region. Has also a slight blue shift for the far-red maximum. Could also absorb green light. May participate in regulating pigment synthesis like the carotenoid deinoxanthin which could protect the bacterium from intense visible light.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Deinococcus radiodurans]]		[[Category: Deinococcus radiodurans]]
-	[[Category: Brunzelle, J S.]]	+	[[Category: Brunzelle, J S]]
-	[[Category: Forest, K T.]]	+	[[Category: Forest, K T]]
-	[[Category: Vierstra, R D.]]	+	[[Category: Vierstra, R D]]
-	[[Category: Wagner, J R.]]	+	[[Category: Wagner, J R]]
	[[Category: Bacteriophytochrome]]		[[Category: Bacteriophytochrome]]
	[[Category: Biliverdin ix]]		[[Category: Biliverdin ix]]

OCA at 01:03, 30 September 2014

OCA — Tue, 30 Sep 2014 01:03:09 GMT

←Older revision		Revision as of 01:03, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1ztu.~~png~~\|~~left~~\|200px]]	+	==Structure of the chromophore binding domain of bacterial phytochrome==
		+	<StructureSection load='1ztu' size='340' side='right' caption='[[1ztu]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ztu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZTU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZTU FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 Deinococcus radiodurans])</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=1ztu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ztu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ztu RCSB], [http://www.ebi.ac.uk/pdbsum/1ztu 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/zt/1ztu_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 ==
		+	Phytochromes are red/far-red light photoreceptors that direct photosensory responses across the bacterial, fungal and plant kingdoms. These include photosynthetic potential and pigmentation in bacteria as well as chloroplast development and photomorphogenesis in plants. Phytochromes consist of an amino-terminal region that covalently binds a single bilin chromophore, followed by a carboxy-terminal dimerization domain that often transmits the light signal through a histidine kinase relay. Here we describe the three-dimensional structure of the chromophore-binding domain of Deinococcus radiodurans phytochrome assembled with its chromophore biliverdin in the Pr ground state. Our model, refined to 2.5 A resolution, reaffirms Cys 24 as the chromophore attachment site, locates key amino acids that form a solvent-shielded bilin-binding pocket, and reveals an unusually formed deep trefoil knot that stabilizes this region. The structure provides the first three-dimensional glimpse into the photochromic behaviour of these photoreceptors and helps to explain the evolution of higher plant phytochromes from prokaryotic precursors.

-	~~{{STRUCTURE_1ztu\| PDB=1ztu \| SCENE= }}~~	+	A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome.,Wagner JR, Brunzelle JS, Forest KT, Vierstra RD Nature. 2005 Nov 17;438(7066):325-31. PMID:16292304<ref>PMID:16292304</ref>

-	~~===Structure~~ of the ~~chromophore binding domain of bacterial phytochrome===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16292304}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1ztu]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1ZTU OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016292304<~~/~~ref~~><~~ref group="xtra">PMID:016978047</ref><references group="xtra"~~/>	+
	[[Category: Deinococcus radiodurans]]		[[Category: Deinococcus radiodurans]]
	[[Category: Brunzelle, J S.]]		[[Category: Brunzelle, J S.]]

OCA: Protected "1ztu" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 17:22:53 GMT

Protected "1ztu" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:22, 5 January 2013

OCA at 17:22, 5 January 2013

OCA — Sat, 05 Jan 2013 17:22:50 GMT

←Older revision		Revision as of 17:22, 5 January 2013
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-	{{Seed}}
	[[Image:1ztu.png\|left\|200px]]		[[Image:1ztu.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1ztu", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1ztu\| PDB=1ztu \| SCENE= }}		{{STRUCTURE_1ztu\| PDB=1ztu \| SCENE= }}

	===Structure of the chromophore binding domain of bacterial phytochrome===		===Structure of the chromophore binding domain of bacterial phytochrome===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16292304}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16292304 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16292304}}		{{ABSTRACT_PUBMED_16292304}}

	==About this Structure==		==About this Structure==
-	~~1ZTU~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZTU OCA].	+	[[1ztu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZTU OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16292304~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016292304</ref><ref group="xtra">PMID:016978047</ref><references group="xtra"/>
	[[Category: Deinococcus radiodurans]]		[[Category: Deinococcus radiodurans]]
	[[Category: Brunzelle, J S.]]		[[Category: Brunzelle, J S.]]
Line 36:		Line 24:
	[[Category: Pa]]		[[Category: Pa]]
	[[Category: Phytochrome]]		[[Category: Phytochrome]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 13:10:05 2009''~~	+

OCA at 11:10, 17 February 2009

OCA — Tue, 17 Feb 2009 11:10:06 GMT

←Older revision		Revision as of 11:10, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1ZTU is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZTU OCA].	+	1ZTU is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZTU OCA].

	==Reference==		==Reference==
-	~~A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome., Wagner JR, Brunzelle JS, Forest KT, Vierstra RD, Nature. 2005 Nov 17;438(7066):325-31.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16292304 16292304]~~	+	<ref group="xtra">PMID:16292304</ref><references group="xtra"/>
	[[Category: Deinococcus radiodurans]]		[[Category: Deinococcus radiodurans]]
-	[[Category: Single protein]]
	[[Category: Brunzelle, J S.]]		[[Category: Brunzelle, J S.]]
	[[Category: Forest, K T.]]		[[Category: Forest, K T.]]
Line 38:		Line 37:
	[[Category: Phytochrome]]		[[Category: Phytochrome]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28~~ 17:41:~~22 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:10:05 2009''