1dbf: Difference between revisions

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OCA

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-[[Image:1dbf.gif|left|200px]]<br /><applet load="1dbf" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1dbf, resolution 1.30&Aring;" />
-'''CHORISMATE MUTASE FROM BACILLUS SUBTILIS AT 1.30 ANGSTROM'''<br />
-==Overview==
+==CHORISMATE MUTASE FROM BACILLUS SUBTILIS AT 1.30 ANGSTROM==
-The crystal structure of the Bacillus subtilis chorismate mutase, an, enzyme of the aromatic amino acids biosynthetic pathway, was determined to, 1.30 A resolution. The structure of the homotrimer was determined by, molecular replacement using orthorhombic crystals of space group, P2(1)2(1)2(1) with unit-cell parameters a = 52.2, b = 83. 8, c = 86.0 A., The ABC trimer of the monoclinic crystal structure [Chook et al. (1994), J. Mol. Biol. 240, 476-500] was used as the starting model. The final, coordinates are composed of three complete polypeptide chains of 127, amino-acid residues. In addition, there are nine sulfate ions, five, glycerol molecules and 424 water molecules clearly visible in the, structure. This structure was refined with aniosotropic temperature, factors, has excellent geometry and a crystallographic R factor of 0.169, with an R(free) of 0.236. The three active sites of the macromolecule are, at the subunit interfaces, with residues from two subunits contributing to, each site. This orthorhombic crystal form was grown using ammonium sulfate, as the precipitant; glycerol was used as a cryoprotectant during data, collection. A glycerol molecule and sulfate ion in each of the active, sites was found mimicking a transition-state analog. In this structure, the C-terminal tails of the subunits of the trimer are hydrogen bonded to, residues of the active site of neighboring trimers in the crystal and thus, cross-link the molecules in the crystal lattice.
+<StructureSection load='1dbf' size='340' side='right'caption='[[1dbf]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1dbf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DBF FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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=1dbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dbf OCA], [https://pdbe.org/1dbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dbf RCSB], [https://www.ebi.ac.uk/pdbsum/1dbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dbf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AROH_BACSU AROH_BACSU] Catalyzes the Claisen rearrangement of chorismate to prephenate. Probably involved in the aromatic amino acid biosynthesis.<ref>PMID:2105742</ref>
+== 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/db/1dbf_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=1dbf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of the Bacillus subtilis chorismate mutase, an enzyme of the aromatic amino acids biosynthetic pathway, was determined to 1.30 A resolution. The structure of the homotrimer was determined by molecular replacement using orthorhombic crystals of space group P2(1)2(1)2(1) with unit-cell parameters a = 52.2, b = 83. 8, c = 86.0 A. The ABC trimer of the monoclinic crystal structure [Chook et al. (1994), J. Mol. Biol. 240, 476-500] was used as the starting model. The final coordinates are composed of three complete polypeptide chains of 127 amino-acid residues. In addition, there are nine sulfate ions, five glycerol molecules and 424 water molecules clearly visible in the structure. This structure was refined with aniosotropic temperature factors, has excellent geometry and a crystallographic R factor of 0.169 with an R(free) of 0.236. The three active sites of the macromolecule are at the subunit interfaces, with residues from two subunits contributing to each site. This orthorhombic crystal form was grown using ammonium sulfate as the precipitant; glycerol was used as a cryoprotectant during data collection. A glycerol molecule and sulfate ion in each of the active sites was found mimicking a transition-state analog. In this structure, the C-terminal tails of the subunits of the trimer are hydrogen bonded to residues of the active site of neighboring trimers in the crystal and thus cross-link the molecules in the crystal lattice.
-==About this Structure==
+The 1.30 A resolution structure of the Bacillus subtilis chorismate mutase catalytic homotrimer.,Ladner JE, Reddy P, Davis A, Tordova M, Howard AJ, Gilliland GL Acta Crystallogr D Biol Crystallogr. 2000 Jun;56(Pt 6):673-83. PMID:10818343<ref>PMID:10818343</ref>
-DBF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with SO4 and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Chorismate_mutase Chorismate mutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.5 5.4.99.5] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DBF OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-The 1.30 A resolution structure of the Bacillus subtilis chorismate mutase catalytic homotrimer., Ladner JE, Reddy P, Davis A, Tordova M, Howard AJ, Gilliland GL, Acta Crystallogr D Biol Crystallogr. 2000 Jun;56(Pt 6):673-83. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10818343 10818343]
+</div>
+<div class="pdbe-citations 1dbf" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[3D structures of chorismate mutase|3D structures of chorismate mutase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Bacillus subtilis]]
-[[Category: Chorismate mutase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Gilliland GL]]
-[[Category: Gilliland, G.L.]]
+[[Category: Ladner JE]]
-[[Category: Ladner, J.E.]]
-[[Category: GOL]]
-[[Category: SO4]]
-[[Category: chorismate mutase]]
-[[Category: shikimate pathway]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:08:16 2007''