7fdr: Difference between revisions

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-{{Seed}}
-[[Image:7fdr.png|left|200px]]
-<!--
+==7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII, NA DITHIONITE REDUCED, PH 8.5, 1.4A RESOLUTION, 100 K==
-The line below this paragraph, containing "STRUCTURE_7fdr", creates the "Structure Box" on the page.
+<StructureSection load='7fdr' size='340' side='right'caption='[[7fdr]], [[Resolution|resolution]] 1.40&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'>[[7fdr]] is a 1 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=7FDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FDR 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]] 1.4&#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_7fdr|  PDB=7fdr  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7fdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fdr OCA], [https://pdbe.org/7fdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7fdr RCSB], [https://www.ebi.ac.uk/pdbsum/7fdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7fdr 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/fd/7fdr_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=7fdr ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The refined structure of reduced Azotobacter vinelandii 7Fe ferredoxin FdI at 100 K and 1.4 A resolution is reported, permitting comparison of [3Fe-4S]+ and [3Fe-4S]0 clusters in the same protein at near atomic resolution. The reduced state of the [3Fe-4S]0 cluster is established by single-crystal EPR following data collection. Redundant structures are refined to establish the reproducibility and accuracy of the results for both oxidation states. The structure of the [4Fe-4S]2+ cluster in four independently determined FdI structures is the same within the range of derived standard uncertainties, providing an internal control on the experimental methods and the refinement results. The structures of the [3Fe-4S]+ and [3Fe-4S]0 clusters are also the same within experimental error, indicating that the protein may be enforcing an entatic state upon this cluster, facilitating electron-transfer reactions. The structure of the FdI [3Fe-4S]0 cluster allows direct comparison with the structure of a well-characterized [Fe3S4]0 synthetic analogue compound. The [3Fe-4S]0 cluster displays significant distortions with respect to the [Fe3S4]0 analogue, further suggesting that the observed [3Fe-4S]+/0 geometry in FdI may represent an entatic state. Comparison of oxidized and reduced FdI reveals conformational changes at the protein surface in response to reduction of the [3Fe-4S]+/0 cluster. The carboxyl group of Asp15 rotates approximately 90 degrees, Lys84, a residue hydrogen bonded to Asp15, adopts a single conformation, and additional H2O molecules become ordered. These structural changes imply a mechanism for H+ transfer to the [3Fe-4S]0 cluster in agreement with electrochemical and spectroscopic results.
-===7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII, NA DITHIONITE REDUCED, PH 8.5, 1.4A RESOLUTION, 100 K===
+Oxidized and reduced Azotobacter vinelandii ferredoxin I at 1.4 A resolution: conformational change of surface residues without significant change in the [3Fe-4S]+/0 cluster.,Schipke CG, Goodin DB, McRee DE, Stout CD Biochemistry. 1999 Jun 29;38(26):8228-39. PMID:10387068<ref>PMID:10387068</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 7fdr" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_10387068}}, adds the Publication Abstract to the page
+*[[Ferredoxin 3D structures|Ferredoxin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 10387068 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10387068}}
+__TOC__
+</StructureSection>
-==About this Structure==
-FDR is a 1 chain structure of sequence 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=7FDR OCA].
-==Reference==
-<ref group="xtra">PMID:10387068</ref><references group="xtra"/>
 [[Category: Azotobacter vinelandii]]
-[[Category: Goodin, D B.]]
+[[Category: Large Structures]]
-[[Category: Mcree, D E.]]
+[[Category: Goodin DB]]
-[[Category: Schipke, C G.]]
+[[Category: Mcree DE]]
-[[Category: Stout, C D.]]
+[[Category: Schipke CG]]
-[[Category: Electron transport]]
+[[Category: Stout CD]]
-[[Category: Iron-sulfur]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 05:49:02 2009''