1lcd: Difference between revisions

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-{{Seed}}
-[[Image:1lcd.png|left|200px]]
-<!--
+==STRUCTURE OF THE COMPLEX OF LAC REPRESSOR HEADPIECE AND AN 11 BASE-PAIR HALF-OPERATOR DETERMINED BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS==
-The line below this paragraph, containing "STRUCTURE_1lcd", creates the "Structure Box" on the page.
+<StructureSection load='1lcd' size='340' side='right'caption='[[1lcd]]' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1lcd]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LCD FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-{{STRUCTURE_1lcd|  PDB=1lcd  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1lcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lcd OCA], [https://pdbe.org/1lcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lcd RCSB], [https://www.ebi.ac.uk/pdbsum/1lcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lcd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LACI_ECOLI LACI_ECOLI] Repressor of the lactose operon. Binds allolactose as an inducer.
+== 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/lc/1lcd_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/main_output.php?pdb_ID=1lcd ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structure of the complex of lac repressor headpiece and an 11 base-pair lac half-operator has been determined by NMR spectroscopy and restrained Molecular Dynamics calculations. In total 508 distances were derived from two-dimensional nuclear Overhauser enhancement measurements, 260 of which are within the headpiece, 212 within the operator and 36 between operator and headpiece. An equilibrium restrained Molecular Dynamics calculation of the complex in aqueous solution, spanning 85 picoseconds, has been used to analyze the structure. Configuration sampling by an annealing procedure has been undertaken as well in order to estimate the precision of the structure determination. Our data confirm the results of previous two-dimensional NMR studies that the orientation of the recognition helix of lac repressor in the major groove of DNA with respect to the operator dyad axis is opposite to the orientation found in complexes of other DNA binding proteins of the helix-turn-helix class. We find a number of tight contacts between the protein and the operator that are in agreement with the available genetic and biochemical data. The anchoring of lac headpiece on the operator is similar to that of other repressors. Other features are unique for lac headpiece: relative few direct hydrogen bonds between side-chains and bases; extensive apolar contacts; many direct and water-bridged contacts to phosphates from residues in or close to the recognition helix. Overall, an interconnected set of interactions is observed, involving base-specific contacts, phosphate contacts, intra-protein and water-bridged hydrogen bonds. Several of these interactions appear to be dynamic, i.e. fluctuating in time, rather than static.
-===STRUCTURE OF THE COMPLEX OF LAC REPRESSOR HEADPIECE AND AN 11 BASE-PAIR HALF-OPERATOR DETERMINED BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS===
+Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics.,Chuprina VP, Rullmann JA, Lamerichs RM, van Boom JH, Boelens R, Kaptein R J Mol Biol. 1993 Nov 20;234(2):446-62. PMID:8230225<ref>PMID:8230225</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1lcd" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_8230225}}, adds the Publication Abstract to the page
+*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]
-(as it appears on PubMed at http://www.pubmed.gov), where 8230225 is the PubMed ID number.
+*[[Lac repressor|Lac repressor]]
--->
+== References ==
-{{ABSTRACT_PUBMED_8230225}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-LCD is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LCD OCA].
-==Reference==
-<ref group="xtra">PMID:8230225</ref><references group="xtra"/>
 [[Category: Escherichia coli]]
-[[Category: Boelens, R.]]
+[[Category: Large Structures]]
-[[Category: Boom, J H.Van.]]
+[[Category: Boelens R]]
-[[Category: Chuprina, V P.]]
+[[Category: Chuprina VP]]
-[[Category: Kaptein, R.]]
+[[Category: Kaptein R]]
-[[Category: Lamerichs, R M.J N.]]
+[[Category: Lamerichs RMJN]]
-[[Category: Rullmann, J A.C.]]
+[[Category: Rullmann JAC]]
-[[Category: Gene regulation/dna]]
+[[Category: Van Boom JH]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:22:22 2009''