1b0v: Difference between revisions

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-{{Seed}}
-[[Image:1b0v.png|left|200px]]
-<!--
+==I40N MUTANT OF AZOTOBACTER VINELANDII FDI==
-The line below this paragraph, containing "STRUCTURE_1b0v", creates the "Structure Box" on the page.
+<StructureSection load='1b0v' size='340' side='right'caption='[[1b0v]], [[Resolution|resolution]] 2.80&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'>[[1b0v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B0V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B0V 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]] 2.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-{{STRUCTURE_1b0v|  PDB=1b0v  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1b0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b0v OCA], [https://pdbe.org/1b0v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b0v RCSB], [https://www.ebi.ac.uk/pdbsum/1b0v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b0v ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FER1_AZOVI FER1_AZOVI] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions. This ferredoxin could play a role in regulating gene expression by interacting directly with DNA.
+== 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/b0/1b0v_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=1b0v ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The [4Fe-4S](2+/+) cluster of Azotobacter vinelandii ferredoxin I (FdI) has an unusually low reduction potential (E(0')) relative to other structurally similar ferredoxins. Previous attempts to raise that E(0') by modification of surface charged residues were unsuccessful. In this study mutants were designed to alter the E(0') by substitution of polar residues for nonpolar residues near the cluster and by modification of backbone amides. Three FdI variants, P21G, I40N, and I40Q, were purified and characterized, and electrochemical E(0') measurements show that all had altered E(0') relative to native FdI. For P21G FdI and I40Q FdI, the E(0') increased by +42 and +53 mV, respectively validating the importance of dipole orientation in control of E(0'). Protein Dipole Langevin Dipole calculations based on models for those variants accurately predicted the direction of the change in E(0') while overestimating the magnitude. For I40N FdI, initial calculations based on the model predicted a +168 mV change in E(0') while a -33 mV change was observed. The x-ray structure of that variant, which was determined to 2.8 A, revealed a number of changes in backbone and side chain dipole orientation and in solvent accessibility, that were not predicted by the model and that were likely to influence E(0'). Subsequent Protein Dipole Langevin Dipole calculations (using the actual I40N x-ray structures) did quite accurately predict the observed change in E(0').
-===I40N MUTANT OF AZOTOBACTER VINELANDII FDI===
+Alteration of the reduction potential of the [4Fe-4S](2+/+) cluster of Azotobacter vinelandii ferredoxin I.,Chen K, Tilley GJ, Sridhar V, Prasad GS, Stout CD, Armstrong FA, Burgess BK J Biol Chem. 1999 Dec 17;274(51):36479-87. PMID:10593945<ref>PMID:10593945</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1b0v" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_10593945}}, adds the Publication Abstract to the page
+*[[Ferredoxin 3D structures|Ferredoxin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 10593945 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10593945}}
+__TOC__
+</StructureSection>
-==About this Structure==
-B0V is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B0V OCA].
-==Reference==
-<ref group="xtra">PMID:10593945</ref><references group="xtra"/>
 [[Category: Azotobacter vinelandii]]
-[[Category: Burgess, B K.]]
+[[Category: Large Structures]]
-[[Category: Chen, K.]]
+[[Category: Burgess BK]]
-[[Category: Prasad, G S.]]
+[[Category: Chen K]]
-[[Category: Sridhar, V.]]
+[[Category: Prasad GS]]
-[[Category: Stout, C D.]]
+[[Category: Sridhar V]]
-[[Category: Electron transport]]
+[[Category: Stout CD]]
-[[Category: Iron-sulfur]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 25 11:00:02 2009''