1per - Revision history

OCA at 08:07, 14 February 2024

2024-02-14T08:07:35Z

←Older revision		Revision as of 08:07, 14 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1per]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PER FirstGlance]. <br>		<table><tr><td colspan='2'>[[1per]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PER FirstGlance]. <br>
-	</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=1per FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1per OCA], [https://pdbe.org/1per PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1per RCSB], [https://www.ebi.ac.uk/pdbsum/1per PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1per ProSAT]</span></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1per FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1per OCA], [https://pdbe.org/1per PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1per RCSB], [https://www.ebi.ac.uk/pdbsum/1per PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1per ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RPC1_BP434 RPC1_BP434]] Binds to two sets of three contiguous operator sites in the phage genome.	+	[https://www.uniprot.org/uniprot/RPC1_BP434 RPC1_BP434] Binds to two sets of three contiguous operator sites in the phage genome.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 18:		Line 19:
	</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=1per 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=1per ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	BACKGROUND: The repressor of phage 434 binds to a set of operator sites as a homodimer. Its relative affinities for these sites determine the switch from lysogenic to lytic growth. The six 434 operator sites (OR1, OR2, OR3, OL1, OL2 and OL3) have a particularly simple organization; all are 14 base pairs long, with a conserved 5'-ACAA sequence symmetrically placed at either end, and a variable central six base pairs. OR3 is unique among naturally-occurring 434 operator sites in that it contains a non-consensus base pair, G.C, at the fourth position of the otherwise invariant 5'-ACAA sequence. Comparisons among structures of the 434 repressor DNA-binding domain, R1-69, bound to various operator sites, allow us to analyze differential specificity in regulatory complexes of this kind. RESULTS: We have determined the structure at 2.5 A resolution of a complex of R1-69 with DNA containing the OR3 site and compared it with previously studied complexes of R1-69 bound to OR1 and OR2. There are surprisingly extensive structural differences between the consensus and non-consensus half-sites of OR3 with respect to their interactions with R1-69, including a shift in the DNA backbone and a small rotation of the entire R1-69 monomer. CONCLUSIONS: Recognition of the base pair difference that is critical for the 434 regulatory switch involves a number of amino acid residues, not just the one or two side chains in direct contact with the G-C base pair. Moreover, the repressor imposes a somewhat altered DNA conformation on the non-consensus half-site.
-
-	The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites.,Rodgers DW, Harrison SC Structure. 1993 Dec 15;1(4):227-40. PMID:8081737<ref>PMID:8081737</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1per" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Bacteriophage repressor\|Bacteriophage repressor]]		*[[Bacteriophage repressor\|Bacteriophage repressor]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Phage 434]]		[[Category: Phage 434]]
-	[[Category: Harrison~~, S C~~]]	+	[[Category: Harrison SC]]
-	[[Category: Rodgers~~, D W]]~~	+	[[Category: Rodgers DW]]
-	~~[[Category: Protein-dna complex]]~~	+
-	~~[[Category: Transcription-dna complex~~]]	+

OCA at 09:28, 8 September 2021

2021-09-08T09:28:50Z

←Older revision		Revision as of 09:28, 8 September 2021
Line 3:		Line 3:
	<StructureSection load='1per' size='340' side='right'caption='[[1per]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1per' size='340' side='right'caption='[[1per]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1per]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1PER FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1per]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PER FirstGlance]. <br>
-	</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=1per FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1per OCA], [~~http~~://pdbe.org/1per PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1per RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1per PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1per ProSAT]</span></td></tr>	+	</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=1per FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1per OCA], [https://pdbe.org/1per PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1per RCSB], [https://www.ebi.ac.uk/pdbsum/1per PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1per ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RPC1_BP434 RPC1_BP434]] Binds to two sets of three contiguous operator sites in the phage genome.	+	[[https://www.uniprot.org/uniprot/RPC1_BP434 RPC1_BP434]] Binds to two sets of three contiguous operator sites in the phage genome.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 30:
	==See Also==		==See Also==
	*[[Bacteriophage repressor\|Bacteriophage repressor]]		*[[Bacteriophage repressor\|Bacteriophage repressor]]
-	*[[Bacteriophage repressor 3D structures\|Bacteriophage repressor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:11, 27 November 2019

2019-11-27T10:11:07Z

←Older revision		Revision as of 10:11, 27 November 2019
Line 1:		Line 1:

	==THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES==		==THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES==
-	<StructureSection load='1per' size='340' side='right' caption='[[1per]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='1per' size='340' side='right'caption='[[1per]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1per]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PER FirstGlance]. <br>		<table><tr><td colspan='2'>[[1per]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PER FirstGlance]. <br>
Line 27:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1per" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1per" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Bacteriophage repressor\|Bacteriophage repressor]]
		+	*[[Bacteriophage repressor 3D structures\|Bacteriophage repressor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Phage 434]]		[[Category: Phage 434]]
	[[Category: Harrison, S C]]		[[Category: Harrison, S C]]

OCA at 07:42, 15 February 2018

2018-02-15T07:42:06Z

←Older revision		Revision as of 07:42, 15 February 2018
Line 1:		Line 1:
		+
	==THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES==		==THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES==
	<StructureSection load='1per' size='340' side='right' caption='[[1per]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1per' size='340' side='right' caption='[[1per]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1per]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bp434 Bp434~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PER FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1per]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PER FirstGlance]. <br>
-	</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=1per FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1per OCA], [http://pdbe.org/1per PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1per RCSB], [http://www.ebi.ac.uk/pdbsum/1per PDBsum]</span></td></tr>	+	</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=1per FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1per OCA], [http://pdbe.org/1per PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1per RCSB], [http://www.ebi.ac.uk/pdbsum/1per PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1per ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pe/1per_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pe/1per_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 26:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1per" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1per" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Bacteriophage repressor\|Bacteriophage repressor]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bp434~~]]	+	[[Category: Phage 434]]
	[[Category: Harrison, S C]]		[[Category: Harrison, S C]]
	[[Category: Rodgers, D W]]		[[Category: Rodgers, D W]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]
	[[Category: Transcription-dna complex]]		[[Category: Transcription-dna complex]]

OCA at 22:19, 9 February 2016

2016-02-09T22:19:26Z

←Older revision		Revision as of 22:19, 9 February 2016
Line 15:		Line 15:
	<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=1per ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:35, 11 September 2015

2015-09-11T02:35:29Z

←Older revision		Revision as of 02:35, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1per' size='340' side='right' caption='[[1per]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1per' size='340' side='right' caption='[[1per]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1per]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Phage_434 Phage 434~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PER FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1per]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bp434 Bp434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PER FirstGlance]. <br>
-	</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=1per FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1per OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1per RCSB], [http://www.ebi.ac.uk/pdbsum/1per PDBsum]</span></td></tr>	+	</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=1per FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1per OCA], [http://pdbe.org/1per PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1per RCSB], [http://www.ebi.ac.uk/pdbsum/1per PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 25:
	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 1per" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Phage 434~~]]	+	[[Category: Bp434]]
	[[Category: Harrison, S C]]		[[Category: Harrison, S C]]
	[[Category: Rodgers, D W]]		[[Category: Rodgers, D W]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]
	[[Category: Transcription-dna complex]]		[[Category: Transcription-dna complex]]

OCA at 09:54, 25 December 2014

2014-12-25T09:54:51Z

←Older revision		Revision as of 09:54, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1per]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PER FirstGlance]. <br>		<table><tr><td colspan='2'>[[1per]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PER FirstGlance]. <br>
-	</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=1per FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1per OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1per RCSB], [http://www.ebi.ac.uk/pdbsum/1per PDBsum]</span></td></tr>	+	</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=1per FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1per OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1per RCSB], [http://www.ebi.ac.uk/pdbsum/1per PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RPC1_BP434 RPC1_BP434]] Binds to two sets of three contiguous operator sites in the phage genome.
	== 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: Phage 434]]		[[Category: Phage 434]]
-	[[Category: Harrison, S C.]]	+	[[Category: Harrison, S C]]
-	[[Category: Rodgers, D W.]]	+	[[Category: Rodgers, D W]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]
	[[Category: Transcription-dna complex]]		[[Category: Transcription-dna complex]]

OCA at 22:53, 28 September 2014

2014-09-28T22:53:19Z

←Older revision		Revision as of 22:53, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1per.~~png\|left~~\|200px]]	+	==THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES==
		+	<StructureSection load='1per' size='340' side='right' caption='[[1per]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1per]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PER FirstGlance]. <br>
		+	</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=1per FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1per OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1per RCSB], [http://www.ebi.ac.uk/pdbsum/1per 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/pe/1per_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 ==
		+	BACKGROUND: The repressor of phage 434 binds to a set of operator sites as a homodimer. Its relative affinities for these sites determine the switch from lysogenic to lytic growth. The six 434 operator sites (OR1, OR2, OR3, OL1, OL2 and OL3) have a particularly simple organization; all are 14 base pairs long, with a conserved 5'-ACAA sequence symmetrically placed at either end, and a variable central six base pairs. OR3 is unique among naturally-occurring 434 operator sites in that it contains a non-consensus base pair, G.C, at the fourth position of the otherwise invariant 5'-ACAA sequence. Comparisons among structures of the 434 repressor DNA-binding domain, R1-69, bound to various operator sites, allow us to analyze differential specificity in regulatory complexes of this kind. RESULTS: We have determined the structure at 2.5 A resolution of a complex of R1-69 with DNA containing the OR3 site and compared it with previously studied complexes of R1-69 bound to OR1 and OR2. There are surprisingly extensive structural differences between the consensus and non-consensus half-sites of OR3 with respect to their interactions with R1-69, including a shift in the DNA backbone and a small rotation of the entire R1-69 monomer. CONCLUSIONS: Recognition of the base pair difference that is critical for the 434 regulatory switch involves a number of amino acid residues, not just the one or two side chains in direct contact with the G-C base pair. Moreover, the repressor imposes a somewhat altered DNA conformation on the non-consensus half-site.

-	~~{{STRUCTURE_1per\| PDB=1per \| SCENE= }}~~	+	The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites.,Rodgers DW, Harrison SC Structure. 1993 Dec 15;1(4):227-40. PMID:8081737<ref>PMID:8081737</ref>

-	~~===THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_8081737}}~~	+	==See Also==
-		+	*[[Bacteriophage repressor\|Bacteriophage repressor]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1per~~]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:008081737<~~/~~ref~~><~~ref group="xtra">PMID:015048824</ref><references group="xtra"~~/>	+
	[[Category: Phage 434]]		[[Category: Phage 434]]
	[[Category: Harrison, S C.]]		[[Category: Harrison, S C.]]

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

2012-12-19T12:13:54Z

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

←Older revision

Revision as of 12:13, 19 December 2012

OCA at 12:13, 19 December 2012

2012-12-19T12:13:53Z

←Older revision		Revision as of 12:13, 19 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1per.png\|left\|200px]]		[[Image:1per.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1per", 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_1per\| PDB=1per \| SCENE= }}		{{STRUCTURE_1per\| PDB=1per \| SCENE= }}

	===THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES===		===THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_8081737}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 8081737 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_8081737}}		{{ABSTRACT_PUBMED_8081737}}

	==About this Structure==		==About this Structure==
-	~~1PER~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA].	+	[[1per]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~8081737~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:008081737</ref><ref group="xtra">PMID:015048824</ref><references group="xtra"/>
	[[Category: Phage 434]]		[[Category: Phage 434]]
	[[Category: Harrison, S C.]]		[[Category: Harrison, S C.]]
	[[Category: Rodgers, D W.]]		[[Category: Rodgers, D W.]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]
-		+	[[Category: Transcription-dna complex]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 13:11:13 2009''~~	+