1dp0: Difference between revisions

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-[[Image:1dp0.gif|left|200px]]
-<!--
+==E. COLI BETA-GALACTOSIDASE AT 1.7 ANGSTROM==
-The line below this paragraph, containing "STRUCTURE_1dp0", creates the "Structure Box" on the page.
+<StructureSection load='1dp0' size='340' side='right'caption='[[1dp0]], [[Resolution|resolution]] 1.70&Aring;' 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'>[[1dp0]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DP0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DP0 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">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-{{STRUCTURE_1dp0|  PDB=1dp0  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dp0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dp0 OCA], [https://pdbe.org/1dp0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dp0 RCSB], [https://www.ebi.ac.uk/pdbsum/1dp0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dp0 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/BGAL_ECOLI BGAL_ECOLI]
+== 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/dp/1dp0_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=1dp0 ConSurf].
+<div style="clear:both"></div>
-'''E. COLI BETA-GALACTOSIDASE AT 1.7 ANGSTROM'''
+==See Also==
+*[[Galactosidase 3D structures|Galactosidase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-The unrefined fold of Escherichia coli beta-galactosidase based on a monoclinic crystal form with four independent tetramers has been reported previously. Here, we describe a new, orthorhombic form with one tetramer per asymmetric unit that has permitted refinement of the structure at 1.7 A resolution. This high-resolution analysis has confirmed the original description of the structure and revealed new details. An essential magnesium ion, identified at the active site in the monoclinic crystals, is also seen in the orthorhombic form. Additional putative magnesium binding sites are also seen. Sodium ions are also known to affect catalysis, and five putative binding sites have been identified, one close to the active site. In a crevice on the protein surface, five linked five-membered solvent rings form a partial clathrate-like structure. Some other unusual aspects of the structure include seven apparent cis-peptide bonds, four of which are proline, and several internal salt-bridge networks. Deep solvent-filled channels and tunnels extend across the surface of the molecule and pass through the center of the tetramer. Because of these departures from a compact globular shape, the molecule is not well characterized by prior empirical relationships between the mass and surface area of proteins. The 50 or so residues at the amino terminus have a largely extended conformation and mostly lie across the surface of the protein. At the same time, however, segment 13-21 contributes to a subunit interface, and residues 29-33 pass through a "tunnel" formed by a domain interface. Taken together, the overall arrangement provides a structural basis for the phenomenon of alpha-complementation.
-==About this Structure==
-DP0 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DP0 OCA].
-==Reference==
-High resolution refinement of beta-galactosidase in a new crystal form reveals multiple metal-binding sites and provides a structural basis for alpha-complementation., Juers DH, Jacobson RH, Wigley D, Zhang XJ, Huber RE, Tronrud DE, Matthews BW, Protein Sci. 2000 Sep;9(9):1685-99. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11045615 11045615]
-[[Category: Beta-galactosidase]]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Huber, R E.]]
+[[Category: Huber RE]]
-[[Category: Jacobson, R H.]]
+[[Category: Jacobson RH]]
-[[Category: Juers, D H.]]
+[[Category: Juers DH]]
-[[Category: Matthews, B W.]]
+[[Category: Matthews BW]]
-[[Category: Tronrud, D E.]]
+[[Category: Tronrud DE]]
-[[Category: Wigley, D.]]
+[[Category: Wigley D]]
-[[Category: Zhang, X J.]]
+[[Category: Zhang XJ]]
-[[Category: Beta supersandwich]]
-[[Category: Immunoglobulin]]
-[[Category: Jelly-roll barrel]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 14:06:06 2008''