3bff: Difference between revisions

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 ==class A beta-lactamase SED-G238C complexed with faropenem==
-<StructureSection load='3bff' size='340' side='right' caption='[[3bff]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='3bff' size='340' side='right'caption='[[3bff]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3bff]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_51115 Atcc 51115]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BFF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BFF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3bff]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Citrobacter_sedlakii Citrobacter sedlakii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BFF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BFF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FPM:(5R,6S)-6-(1-HYDROXYETHYL)-7-OXO-3-[(2R)-OXOLAN-2-YL]-4-THIA-1-AZABICYCLO[3.2.0]HEPT-2-ENE-2-CARBOXYLIC+ACID'>FPM</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=SFR:(2R)-2-[(1S,2R)-1-CARBOXY-2-HYDROXYPROPYL]-5-[(2R)-TETRAHYDROFURAN-2-YL]-2,3-DIHYDRO-1,3-THIAZOLE-4-CARBOXYLIC+ACID'>SFR</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]] 1.9&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3bfc|3bfc]], [[3bfd|3bfd]], [[3bfe|3bfe]], [[3bfg|3bfg]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FPM:(5R,6S)-6-(1-HYDROXYETHYL)-7-OXO-3-[(2R)-OXOLAN-2-YL]-4-THIA-1-AZABICYCLO[3.2.0]HEPT-2-ENE-2-CARBOXYLIC+ACID'>FPM</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=SFR:(2R)-2-[(1S,2R)-1-CARBOXY-2-HYDROXYPROPYL]-5-[(2R)-OXOLAN-2-YL]-2,3-DIHYDRO-1,3-THIAZOLE-4-CARBOXYLIC+ACID'>SFR</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bla-SED-1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=67826 ATCC 51115])</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=3bff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bff OCA], [https://pdbe.org/3bff PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bff RCSB], [https://www.ebi.ac.uk/pdbsum/3bff PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bff ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bff OCA], [http://pdbe.org/3bff PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bff RCSB], [http://www.ebi.ac.uk/pdbsum/3bff PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q93PQ0_9ENTR Q93PQ0_9ENTR]
 == 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/bf/3bff_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bf/3bff_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3bff ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-SED-1, a class A beta-lactamase from Citrobacter sedlakii, is a CTX-M-type extended-spectrum beta-lactamase that has the ability to hydrolyze expanded-spectrum cephalosporins such as cefotaxime. SED-1 and a SED mutant in which Gly238 has been replaced by a cysteine, forming a disulfide bridge with the other Cys residue located at position 69 (SED-G238C), have been crystallized. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 188.09, b = 73.65, c = 105.41 A, beta = 121.67 degrees for SED-1 and a = 187.64, b = 73.2, c = 103.89 A, beta = 121.89 degrees for the SED-G238C mutant. X-ray diffraction data were collected to maximum resolutions of 2.4 A for SED-1 and 2.0 A for SED-G238C.
-Crystallization and preliminary X-ray diffraction study of the class A beta-lactamase SED-1 and its mutant SED-G238C from Citrobacter sedlakii.,Petrella S, Pernot L, Sougakoff W Acta Crystallogr D Biol Crystallogr. 2004 Jan;60(Pt 1):125-8. Epub 2003, Dec 18. PMID:14684905<ref>PMID:14684905</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3bff" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Beta-lactamase|Beta-lactamase]]
+*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 51115]]
+[[Category: Citrobacter sedlakii]]
-[[Category: Beta-lactamase]]
+[[Category: Large Structures]]
-[[Category: Pernot, L]]
+[[Category: Pernot L]]
-[[Category: Petrella, S]]
+[[Category: Petrella S]]
-[[Category: Sougakoff, W]]
+[[Category: Sougakoff W]]
-[[Category: Acyl-enzyme]]
-[[Category: Class a sed-g238c]]
-[[Category: Faropenem]]
-[[Category: Hydrolase]]