3dp5: Difference between revisions

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-{{Seed}}
-[[Image:3dp5.png|left|200px]]
-<!--
+==Crystal structure of Geobacter sulfurreducens OmcF with N-terminal Strep-tag II==
-The line below this paragraph, containing "STRUCTURE_3dp5", creates the "Structure Box" on the page.
+<StructureSection load='3dp5' size='340' side='right'caption='[[3dp5]], [[Resolution|resolution]] 1.86&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'>[[3dp5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacter_sulfurreducens Geobacter sulfurreducens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DP5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DP5 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]] 1.86&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3dp5|  PDB=3dp5  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dp5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dp5 OCA], [https://pdbe.org/3dp5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dp5 RCSB], [https://www.ebi.ac.uk/pdbsum/3dp5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dp5 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q74AE4_GEOSL Q74AE4_GEOSL]
+== 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/3dp5_consurf.spt"</scriptWhenChecked>
+    <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=3dp5 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The putative outer membrane c-type cytochrome OmcF from Geobacter sulfurreducens contains a single haem group and shows homology to soluble cytochromes c(6), a class of electron-transfer proteins that are typically found in cyanobacterial photosynthetic electron-transfer chains. OmcF was overexpressed heterologously in Escherichia coli as an N-terminal Strep-tag II fusion protein and isolated using streptactin-affinity chromatography followed by size-exclusion chromatography. The structure was solved by Fe SAD using data collected to a resolution of 1.86 A on a rotating copper-anode X-ray generator. In the crystal, packing interactions in one dimension were exclusively mediated through the Strep-tag II sequence. The tag and linker regions were in contact with three further monomers of OmcF, leading to a well defined electron-density map for this engineered and secondary-structure-free region of the molecule.
-===Crystal structure of Geobacter sulfurreducens OmcF with N-terminal Strep-tag II===
+Crystal packing of the c(6)-type cytochrome OmcF from Geobacter sulfurreducens is mediated by an N-terminal Strep-tag II.,Lukat P, Hoffmann M, Einsle O Acta Crystallogr D Biol Crystallogr. 2008 Sep;64(Pt 9):919-26. Epub 2008, Aug 13. PMID:18703839<ref>PMID:18703839</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18703839}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3dp5" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18703839 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18703839}}
+__TOC__
+</StructureSection>
-==About this Structure==
-DP5 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Geobacter_sulfurreducens Geobacter sulfurreducens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DP5 OCA].
-==Reference==
-<ref group="xtra">PMID:18703839</ref><references group="xtra"/>
 [[Category: Geobacter sulfurreducens]]
-[[Category: Einsle, O.]]
+[[Category: Large Structures]]
-[[Category: Hoffmann, M.]]
+[[Category: Einsle O]]
-[[Category: Lukat, P.]]
+[[Category: Hoffmann M]]
-[[Category: C-type cytochrome]]
+[[Category: Lukat P]]
-[[Category: Dissimilatory metal reduction]]
-[[Category: Electron transport]]
-[[Category: Fe sad phasing]]
-[[Category: Geobacter sulfurreducen]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 13:02:53 2009''