3soi: Difference between revisions

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 <StructureSection load='3soi' size='340' side='right'caption='[[3soi]], [[Resolution|resolution]] 1.73&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3soi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"denitrobacillus_licheniformis"_(weigmann_1898)_verhoeven_1952 "denitrobacillus licheniformis" (weigmann 1898) verhoeven 1952]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SOI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SOI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3soi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_licheniformis Bacillus licheniformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SOI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SOI FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</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]] 1.729&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4blm|4blm]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">penP, blaP ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1402 "Denitrobacillus licheniformis" (Weigmann 1898) Verhoeven 1952])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></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=3soi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3soi OCA], [https://pdbe.org/3soi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3soi RCSB], [https://www.ebi.ac.uk/pdbsum/3soi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3soi ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/BLAC_BACLI BLAC_BACLI]
-beta-lactamases confer antibiotic resistance, one of the most serious world-wide health problems, and are an excellent theoretical and experimental model in the study of protein structure, dynamics and evolution. Bacillus licheniformis exo-small penicillinase (ESP) is a Class-A beta-lactamase with three tryptophan residues located in the protein core. Here, we report the 1.7-A resolution X-ray structure, catalytic parameters, and thermodynamic stability of ESP(DeltaW), an engineered mutant of ESP in which phenylalanine replaces the wild-type tryptophan residues. The structure revealed no qualitative conformational changes compared with thirteen previously reported structures of B. licheniformis beta-lactamases (RMSD = 0.4-1.2 A). However, a closer scrutiny showed that the mutations result in an overall more compact structure, with most atoms shifted toward the geometric center of the molecule. Thus, ESP(DeltaW) has a significantly smaller radius of gyration (R(g)) than the other B. licheniformis beta-lactamases characterized so far. Indeed, ESP(DeltaW) has the smallest R(g) among 126 Class-A beta-lactamases in the Protein Data Bank (PDB). Other measures of compactness, like the number of atoms in fixed volumes and the number and average of noncovalent distances, confirmed the effect. ESP(DeltaW) proves that the compactness of the native state can be enhanced by protein engineering and establishes a new lower limit to the compactness of the Class-A beta-lactamase fold. As the condensation achieved by the native state is a paramount notion in protein folding, this result may contribute to a better understanding of how the sequence determines the conformational variability and thermodynamic stability of a given fold.
-X-ray evidence of a native state with increased compactness populated by tryptophan-less B. licheniformis beta-lactamase.,Risso VA, Acierno JP, Capaldi S, Monaco HL, Ermacora MR Protein Sci. 2012 Jul;21(7):964-76. doi: 10.1002/pro.2076. Epub 2012 May 31. PMID:22496053<ref>PMID:22496053</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3soi" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Beta-lactamase]]
+[[Category: Bacillus licheniformis]]
 [[Category: Large Structures]]
-[[Category: Acierno, J P]]
+[[Category: Acierno JP]]
-[[Category: Capaldi, S]]
+[[Category: Capaldi S]]
-[[Category: Ermacora, M R]]
+[[Category: Ermacora MR]]
-[[Category: Monaco, H L]]
+[[Category: Monaco HL]]
-[[Category: Risso, V A]]
+[[Category: Risso VA]]
-[[Category: Hydrolase]]