6cro: Difference between revisions

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 ==CRYSTAL STRUCTURE OF LAMBDA-CRO BOUND TO A CONSENSUS OPERATOR AT 3.0 ANGSTROM RESOLUTION==
-<StructureSection load='6cro' size='340' side='right' caption='[[6cro]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='6cro' size='340' side='right'caption='[[6cro]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6cro]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_lambda Bacteriophage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CRO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CRO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6cro]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_Lambda Escherichia virus Lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CRO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CRO FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</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=6cro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cro OCA], [http://pdbe.org/6cro PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cro RCSB], [http://www.ebi.ac.uk/pdbsum/6cro PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cro ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=6cro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cro OCA], [https://pdbe.org/6cro PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cro RCSB], [https://www.ebi.ac.uk/pdbsum/6cro PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cro ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RCRO_LAMBD RCRO_LAMBD]] Cro represses genes normally expressed in early phage development and is necessary for the late stage of lytic growth. It does this by binding to the OL and OR operators regions normally used by the repressor protein for lysogenic maintenance.
+[https://www.uniprot.org/uniprot/RCRO_LAMBD RCRO_LAMBD] Cro represses genes normally expressed in early phage development and is necessary for the late stage of lytic growth. It does this by binding to the OL and OR operators regions normally used by the repressor protein for lysogenic maintenance.
 == 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/cr/6cro_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cr/6cro_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 19: / Line 20: @@
 </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=6cro ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The structure of the Cro protein from bacteriophage lambda in complex with a 19 base-pair DNA duplex that includes the 17 base-pair consensus operator has been determined at 3.0 A resolution. The structure confirms the large changes in the protein and DNA seen previously in a crystallographically distinct low-resolution structure of the complex and, for the first time, reveals the detailed interactions between the side-chains of the protein and the base-pairs of the operator. Relative to the crystal structure of the free protein, the subunits of Cro rotate 53 degrees with respect to each other on binding DNA. At the same time the DNA is bent by 40 degrees through the 19 base-pairs. The intersubunit connection includes a region within the protein core that is structurally reminiscent of the "ball and socket" motif seen in the immunoglobulins and T-cell receptors. The crystal structure of the Cro complex is consistent with virtually all available biochemical and related data. Some of the interactions between Cro and DNA proposed on the basis of model-building are now seen to be correct, but many are different. Tests of the original model by mutagenesis and biochemical analysis corrected some but not all of the errors. Within the limitations of the crystallographic resolution it appears that operator recognition is achieved almost entirely by direct hydrogen-bonding and van der Waals contacts between the protein and the exposed bases within the major groove of the DNA. The discrimination of Cro between the operators OR3 and OR1, which differ in sequence at just three positions, is inferred to result from a combination of small differences, both favorable and unfavorable. A van der Waals contact at one of the positions is of primary importance, while the other two provide smaller, indirect effects. Direct hydrogen bonding is not utilized in this distinction.
-Crystal structure of lambda-Cro bound to a consensus operator at 3.0 A resolution.,Albright RA, Matthews BW J Mol Biol. 1998 Jul 3;280(1):137-51. PMID:9653037<ref>PMID:9653037</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 6cro" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[User:Wayne Decatur/Tomato aspermy virus protein 2b Suppression of RNA Silencing|User:Wayne Decatur/Tomato aspermy virus protein 2b Suppression of RNA Silencing]]
+*[[Tomato aspermy virus protein 2b Suppression of RNA Silencing|Tomato aspermy virus protein 2b Suppression of RNA Silencing]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacteriophage lambda]]
+[[Category: Escherichia virus Lambda]]
-[[Category: Albright, R A]]
+[[Category: Large Structures]]
-[[Category: Matthews, B W]]
+[[Category: Albright RA]]
-[[Category: Conformational change]]
+[[Category: Matthews BW]]
-[[Category: Cro]]
-[[Category: Gene regulation-dna complex]]
-[[Category: Helix-turn-helix]]
-[[Category: Repressor]]