2fa1: Difference between revisions

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 ==Crystal structure of PhnF C-terminal domain==
-<StructureSection load='2fa1' size='340' side='right' caption='[[2fa1]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+<StructureSection load='2fa1' size='340' side='right'caption='[[2fa1]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2fa1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FA1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FA1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2fa1]] is a 2 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=2FA1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FA1 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BDF:BETA-D-FRUCTOPYRANOSE'>BDF</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]] 1.7&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">phnF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BDF:BETA-D-FRUCTOPYRANOSE'>BDF</scene></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=2fa1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fa1 OCA], [http://pdbe.org/2fa1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fa1 RCSB], [http://www.ebi.ac.uk/pdbsum/2fa1 PDBsum], [http://www.topsan.org/Proteins/MCSG/2fa1 TOPSAN]</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=2fa1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fa1 OCA], [https://pdbe.org/2fa1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fa1 RCSB], [https://www.ebi.ac.uk/pdbsum/2fa1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fa1 ProSAT], [https://www.topsan.org/Proteins/MCSG/2fa1 TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PHNF_ECOLI PHNF_ECOLI]] Belongs to an operon involved in alkylphosphonate uptake and C-P lyase. Exact function not known. By similarity could be a transcriptional regulator.
+[https://www.uniprot.org/uniprot/PHNF_ECOLI PHNF_ECOLI] Belongs to an operon involved in alkylphosphonate uptake and C-P lyase. Exact function not known. By similarity could be a transcriptional regulator.
 == 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/fa/2fa1_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fa/2fa1_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2fa1 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The crystal structure of Escherichia coli PhnF C-terminal domain (C-PhnF) was solved at 1.7 A resolution by the single wavelength anomalous dispersion (SAD) method. The PhnF protein belongs to the HutC subfamily of the large GntR transcriptional regulator family. Members of this family share similar N-terminal DNA-binding domains, but are divided into four subfamilies according to their heterogenic C-terminal domains, which are involved in effector binding and oligomerization. The C-PhnF structure provides for the first time the scaffold of this domain for the HutC subfamily, which covers about 31% of GntR-like regulators. The structure represents a mixture of alpha-helices and beta-strands, with a six-stranded antiparallel beta-sheet at the core. C-PhnF monomers form a dimer by establishing interdomain eight-strand beta-sheets that include core antiparallel and N-terminal two-strand parallel beta-sheets from each monomer. C-PhnF shares strong structural similarity with the chorismate lyase fold, which features a buried active site locked behind two helix-turn-helix loops. The structural comparison of the C-PhnF and UbiC proteins allows us to propose that a similar site in the PhnF structure is adapted for effector binding.
-Structural characterization of GntR/HutC family signaling domain.,Gorelik M, Lunin VV, Skarina T, Savchenko A Protein Sci. 2006 Jun;15(6):1506-11. Epub 2006 May 2. PMID:16672238<ref>PMID:16672238</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2fa1" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Edwards, A M]]
+[[Category: Large Structures]]
-[[Category: Gorelik, M]]
+[[Category: Edwards AM]]
-[[Category: Joachimiak, A]]
+[[Category: Gorelik M]]
-[[Category: Lunin, V V]]
+[[Category: Joachimiak A]]
-[[Category: Structural genomic]]
+[[Category: Lunin VV]]
-[[Category: Nocek, B P]]
+[[Category: Nocek BP]]
-[[Category: Savchenko, A]]
+[[Category: Savchenko A]]
-[[Category: Skarina, T]]
+[[Category: Skarina T]]
-[[Category: Apc5558]]
-[[Category: Effector binding domain]]
-[[Category: Mcsg]]
-[[Category: Pnhf]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Regulator]]
-[[Category: Transcription]]