1pra - Revision history

OCA at 09:00, 22 May 2024

OCA — Wed, 22 May 2024 09:00:14 GMT

←Older revision		Revision as of 09:00, 22 May 2024
Line 19:		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=1pra 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=1pra ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The DNA-binding domain of the phage 434 repressor consisting of N-terminal residues 1 to 69 (434 repressor(1-69)), was expressed in Escherichia coli with natural isotope abundance, uniform 15N-labeling and biosynthetically directed fractional 13C-labeling in extent of about 10%. With these protein preparations the three-dimensional structure was determined in solution. The techniques used were nuclear magnetic resonance (n.m.r.) spectroscopy for the collection of conformational constraints, calculation of the protein structure from the n.m.r. data with the program DIANA and structure refinements by restrained energy minimization with a modified version of the program AMBER. A group of 20 conformers characterizes a well-defined structure for residues 1 to 63, with an average of 0-6 A for the root-mean-square deviations (RMSD) calculated for the backbone atoms of the individual conformers relative to the mean co-ordinates. The spatial structure of C-terminal residues 64 to 69 is not defined by the n.m.r. data. The molecular architecture of the 434 repressor(1-69) in solution includes five alpha-helices extending from residues 2 to 13, 17 to 24, 28 to 35, 45 to 52 and 56 to 60, which enclose a well-defined hydrophobic core. The n.m.r. structure is closely similar to the reported crystal structure of the 434 repressor(1-69), with an RMSD value of 1.1 A for the backbone atoms of residues 1 to 63. Small differences between the two structures in regions of the first helix and the loop between helices 3 and 4 were analyzed relative to possible correlations with protein-protein contacts in the crystal lattice and the different milieus of pH and ionic strength in the crystals and n.m.r. samples. Further systematic comparisons of local conformational features indicated that there are correlations between amino acid types, local precision of the structure determination by both techniques and local differences between the structures in the crystals and in solution. Overall, hydrophobic residues are most precisely characterized and agree most closely in the two environments.
		+
		+	Determination of the nuclear magnetic resonance solution structure of the DNA-binding domain (residues 1 to 69) of the 434 repressor and comparison with the X-ray crystal structure.,Neri D, Billeter M, Wuthrich K J Mol Biol. 1992 Feb 5;223(3):743-67. PMID:1311771<ref>PMID:1311771</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1pra" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:58, 17 April 2024

OCA — Wed, 17 Apr 2024 05:58:16 GMT

←Older revision		Revision as of 05:58, 17 April 2024
Line 1:		Line 1:

	==DETERMINATION OF THE NUCLEAR MAGNETIC RESONANCE SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN (RESIDUES 1 TO 69) OF THE 434 REPRESSOR AND COMPARISON WITH THE X-RAY CRYSTAL STRUCTURE==		==DETERMINATION OF THE NUCLEAR MAGNETIC RESONANCE SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN (RESIDUES 1 TO 69) OF THE 434 REPRESSOR AND COMPARISON WITH THE X-RAY CRYSTAL STRUCTURE==
-	<StructureSection load='1pra' size='340' side='right'caption='[[1pra~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='1pra' size='340' side='right'caption='[[1pra]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pra]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bp434 Bp434~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PRA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PRA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pra]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PRA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PRA 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=1pra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pra OCA], [https://pdbe.org/1pra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pra RCSB], [https://www.ebi.ac.uk/pdbsum/1pra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pra ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1pra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pra OCA], [https://pdbe.org/1pra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pra RCSB], [https://www.ebi.ac.uk/pdbsum/1pra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pra 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=1pra 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=1pra ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The DNA-binding domain of the phage 434 repressor consisting of N-terminal residues 1 to 69 (434 repressor(1-69)), was expressed in Escherichia coli with natural isotope abundance, uniform 15N-labeling and biosynthetically directed fractional 13C-labeling in extent of about 10%. With these protein preparations the three-dimensional structure was determined in solution. The techniques used were nuclear magnetic resonance (n.m.r.) spectroscopy for the collection of conformational constraints, calculation of the protein structure from the n.m.r. data with the program DIANA and structure refinements by restrained energy minimization with a modified version of the program AMBER. A group of 20 conformers characterizes a well-defined structure for residues 1 to 63, with an average of 0-6 A for the root-mean-square deviations (RMSD) calculated for the backbone atoms of the individual conformers relative to the mean co-ordinates. The spatial structure of C-terminal residues 64 to 69 is not defined by the n.m.r. data. The molecular architecture of the 434 repressor(1-69) in solution includes five alpha-helices extending from residues 2 to 13, 17 to 24, 28 to 35, 45 to 52 and 56 to 60, which enclose a well-defined hydrophobic core. The n.m.r. structure is closely similar to the reported crystal structure of the 434 repressor(1-69), with an RMSD value of 1.1 A for the backbone atoms of residues 1 to 63. Small differences between the two structures in regions of the first helix and the loop between helices 3 and 4 were analyzed relative to possible correlations with protein-protein contacts in the crystal lattice and the different milieus of pH and ionic strength in the crystals and n.m.r. samples. Further systematic comparisons of local conformational features indicated that there are correlations between amino acid types, local precision of the structure determination by both techniques and local differences between the structures in the crystals and in solution. Overall, hydrophobic residues are most precisely characterized and agree most closely in the two environments.
-
-	Determination of the nuclear magnetic resonance solution structure of the DNA-binding domain (residues 1 to 69) of the 434 repressor and comparison with the X-ray crystal structure.,Neri D, Billeter M, Wuthrich K J Mol Biol. 1992 Feb 5;223(3):743-67. PMID:1311771<ref>PMID:1311771</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1pra" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bp434]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Billeter, M~~]]	+	[[Category: Phage 434]]
-	[[Category: ~~Neri, D~~]]	+	[[Category: Billeter M]]
-	[[Category: ~~Wuthrich, K~~]]	+	[[Category: Neri D]]
-	[[Category: ~~Gene regulating protein~~]]	+	[[Category: Wuthrich K]]

OCA at 09:33, 8 September 2021

OCA — Wed, 08 Sep 2021 09:33:39 GMT

←Older revision		Revision as of 09:33, 8 September 2021
Line 3:		Line 3:
	<StructureSection load='1pra' size='340' side='right'caption='[[1pra]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1pra' size='340' side='right'caption='[[1pra]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pra]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bp434 Bp434]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PRA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1PRA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pra]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bp434 Bp434]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PRA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PRA 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=1pra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pra OCA], [~~http~~://pdbe.org/1pra PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1pra RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1pra PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1pra 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=1pra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pra OCA], [https://pdbe.org/1pra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pra RCSB], [https://www.ebi.ac.uk/pdbsum/1pra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pra 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 27:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1pra" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1pra" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Bacteriophage repressor 3D structures\|Bacteriophage repressor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:15, 27 November 2019

OCA — Wed, 27 Nov 2019 10:15:26 GMT

←Older revision		Revision as of 10:15, 27 November 2019
Line 1:		Line 1:

	==DETERMINATION OF THE NUCLEAR MAGNETIC RESONANCE SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN (RESIDUES 1 TO 69) OF THE 434 REPRESSOR AND COMPARISON WITH THE X-RAY CRYSTAL STRUCTURE==		==DETERMINATION OF THE NUCLEAR MAGNETIC RESONANCE SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN (RESIDUES 1 TO 69) OF THE 434 REPRESSOR AND COMPARISON WITH THE X-RAY CRYSTAL STRUCTURE==
-	<StructureSection load='1pra' size='340' side='right' caption='[[1pra]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='1pra' size='340' side='right'caption='[[1pra]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pra]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bp434 Bp434]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PRA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PRA FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pra]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bp434 Bp434]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PRA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PRA FirstGlance]. <br>
Line 27:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1pra" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1pra" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Bacteriophage repressor 3D structures\|Bacteriophage repressor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 32:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Bp434]]		[[Category: Bp434]]
		+	[[Category: Large Structures]]
	[[Category: Billeter, M]]		[[Category: Billeter, M]]
	[[Category: Neri, D]]		[[Category: Neri, D]]
	[[Category: Wuthrich, K]]		[[Category: Wuthrich, K]]
	[[Category: Gene regulating protein]]		[[Category: Gene regulating protein]]

OCA at 08:15, 24 February 2018

OCA — Sat, 24 Feb 2018 08:15:16 GMT

←Older revision		Revision as of 08:15, 24 February 2018
Line 1:		Line 1:
		+
	==DETERMINATION OF THE NUCLEAR MAGNETIC RESONANCE SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN (RESIDUES 1 TO 69) OF THE 434 REPRESSOR AND COMPARISON WITH THE X-RAY CRYSTAL STRUCTURE==		==DETERMINATION OF THE NUCLEAR MAGNETIC RESONANCE SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN (RESIDUES 1 TO 69) OF THE 434 REPRESSOR AND COMPARISON WITH THE X-RAY CRYSTAL STRUCTURE==
	<StructureSection load='1pra' size='340' side='right' caption='[[1pra]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1pra' size='340' side='right' caption='[[1pra]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pra]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bp434 Bp434]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PRA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PRA FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pra]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bp434 Bp434]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PRA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PRA 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=1pra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pra OCA], [http://pdbe.org/1pra PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pra RCSB], [http://www.ebi.ac.uk/pdbsum/1pra 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=1pra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pra OCA], [http://pdbe.org/1pra PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pra RCSB], [http://www.ebi.ac.uk/pdbsum/1pra PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pra 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/pr/1pra_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pr/1pra_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>
	</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=1pra ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1pra" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1pra" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Bacteriophage repressor\|Bacteriophage repressor]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:53, 11 September 2015

OCA — Fri, 11 Sep 2015 07:53:06 GMT

←Older revision		Revision as of 07:53, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1pra' size='340' side='right' caption='[[1pra]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1pra' size='340' side='right' caption='[[1pra]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pra]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Phage_434 Phage 434~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PRA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PRA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pra]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bp434 Bp434]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PRA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PRA 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=1pra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pra OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pra RCSB], [http://www.ebi.ac.uk/pdbsum/1pra 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=1pra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pra OCA], [http://pdbe.org/1pra PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pra RCSB], [http://www.ebi.ac.uk/pdbsum/1pra 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 1pra" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Phage 434~~]]	+	[[Category: Bp434]]
	[[Category: Billeter, M]]		[[Category: Billeter, M]]
	[[Category: Neri, D]]		[[Category: Neri, D]]
	[[Category: Wuthrich, K]]		[[Category: Wuthrich, K]]
	[[Category: Gene regulating protein]]		[[Category: Gene regulating protein]]

OCA at 13:29, 25 December 2014

OCA — Thu, 25 Dec 2014 13:29:54 GMT

←Older revision		Revision as of 13:29, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pra]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PRA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PRA FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pra]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PRA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PRA 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=1pra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pra OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pra RCSB], [http://www.ebi.ac.uk/pdbsum/1pra 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=1pra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pra OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pra RCSB], [http://www.ebi.ac.uk/pdbsum/1pra 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: Billeter, M.]]	+	[[Category: Billeter, M]]
-	[[Category: Neri, D.]]	+	[[Category: Neri, D]]
-	[[Category: Wuthrich, K.]]	+	[[Category: Wuthrich, K]]
	[[Category: Gene regulating protein]]		[[Category: Gene regulating protein]]

OCA at 22:27, 28 September 2014

OCA — Sun, 28 Sep 2014 22:27:11 GMT

←Older revision		Revision as of 22:27, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1pra.~~png\|left~~\|200px]]	+	==DETERMINATION OF THE NUCLEAR MAGNETIC RESONANCE SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN (RESIDUES 1 TO 69) OF THE 434 REPRESSOR AND COMPARISON WITH THE X-RAY CRYSTAL STRUCTURE==
		+	<StructureSection load='1pra' size='340' side='right' caption='[[1pra]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1pra]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PRA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PRA 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=1pra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pra OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pra RCSB], [http://www.ebi.ac.uk/pdbsum/1pra 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/pr/1pra_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 DNA-binding domain of the phage 434 repressor consisting of N-terminal residues 1 to 69 (434 repressor(1-69)), was expressed in Escherichia coli with natural isotope abundance, uniform 15N-labeling and biosynthetically directed fractional 13C-labeling in extent of about 10%. With these protein preparations the three-dimensional structure was determined in solution. The techniques used were nuclear magnetic resonance (n.m.r.) spectroscopy for the collection of conformational constraints, calculation of the protein structure from the n.m.r. data with the program DIANA and structure refinements by restrained energy minimization with a modified version of the program AMBER. A group of 20 conformers characterizes a well-defined structure for residues 1 to 63, with an average of 0-6 A for the root-mean-square deviations (RMSD) calculated for the backbone atoms of the individual conformers relative to the mean co-ordinates. The spatial structure of C-terminal residues 64 to 69 is not defined by the n.m.r. data. The molecular architecture of the 434 repressor(1-69) in solution includes five alpha-helices extending from residues 2 to 13, 17 to 24, 28 to 35, 45 to 52 and 56 to 60, which enclose a well-defined hydrophobic core. The n.m.r. structure is closely similar to the reported crystal structure of the 434 repressor(1-69), with an RMSD value of 1.1 A for the backbone atoms of residues 1 to 63. Small differences between the two structures in regions of the first helix and the loop between helices 3 and 4 were analyzed relative to possible correlations with protein-protein contacts in the crystal lattice and the different milieus of pH and ionic strength in the crystals and n.m.r. samples. Further systematic comparisons of local conformational features indicated that there are correlations between amino acid types, local precision of the structure determination by both techniques and local differences between the structures in the crystals and in solution. Overall, hydrophobic residues are most precisely characterized and agree most closely in the two environments.

-	~~{{STRUCTURE_1pra\| PDB=1pra \| SCENE= }}~~	+	Determination of the nuclear magnetic resonance solution structure of the DNA-binding domain (residues 1 to 69) of the 434 repressor and comparison with the X-ray crystal structure.,Neri D, Billeter M, Wuthrich K J Mol Biol. 1992 Feb 5;223(3):743-67. PMID:1311771<ref>PMID:1311771</ref>

-	~~===DETERMINATION OF THE NUCLEAR MAGNETIC RESONANCE SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN (RESIDUES 1 TO 69) OF THE 434 REPRESSOR AND COMPARISON WITH THE X-RAY CRYSTAL STRUCTURE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_1311771}}~~	+	==See Also==
-		+	*[[Bacteriophage repressor\|Bacteriophage repressor]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1pra~~]] ~~is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PRA OCA].~~	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:001311771<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Phage 434]]		[[Category: Phage 434]]
	[[Category: Billeter, M.]]		[[Category: Billeter, M.]]

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

OCA — Wed, 19 Dec 2012 11:50:04 GMT

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

←Older revision

Revision as of 11:50, 19 December 2012

OCA at 11:50, 19 December 2012

OCA — Wed, 19 Dec 2012 11:50:01 GMT

←Older revision		Revision as of 11:50, 19 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1pra.png\|left\|200px]]		[[Image:1pra.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1pra", 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_1pra\| PDB=1pra \| SCENE= }}		{{STRUCTURE_1pra\| PDB=1pra \| SCENE= }}

	===DETERMINATION OF THE NUCLEAR MAGNETIC RESONANCE SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN (RESIDUES 1 TO 69) OF THE 434 REPRESSOR AND COMPARISON WITH THE X-RAY CRYSTAL STRUCTURE===		===DETERMINATION OF THE NUCLEAR MAGNETIC RESONANCE SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN (RESIDUES 1 TO 69) OF THE 434 REPRESSOR AND COMPARISON WITH THE X-RAY CRYSTAL STRUCTURE===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_1311771}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 1311771 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_1311771}}		{{ABSTRACT_PUBMED_1311771}}

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

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~1311771~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:001311771</ref><references group="xtra"/>
	[[Category: Phage 434]]		[[Category: Phage 434]]
	[[Category: Billeter, M.]]		[[Category: Billeter, M.]]
Line 29:		Line 17:
	[[Category: Wuthrich, K.]]		[[Category: Wuthrich, K.]]
	[[Category: Gene regulating protein]]		[[Category: Gene regulating protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:26:51 2009''