6fdr

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(New page: 200px<br /><applet load="6fdr" size="450" color="white" frame="true" align="right" spinBox="true" caption="6fdr, resolution 1.4&Aring;" /> '''7-FE FERREDOXIN FROM ...)
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[[Image:6fdr.gif|left|200px]]<br /><applet load="6fdr" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="6fdr, resolution 1.4&Aring;" />
 
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'''7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT 100K, NA DITHIONITE REDUCED AT PH 8.5, RESOLUTION 1.4 A'''<br />
 
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==Overview==
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==7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT 100K, NA DITHIONITE REDUCED AT PH 8.5, RESOLUTION 1.4 A==
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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.
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<StructureSection load='6fdr' size='340' side='right'caption='[[6fdr]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[6fdr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fdc 1fdc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6FDR FirstGlance]. <br>
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</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>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6fdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fdr OCA], [https://pdbe.org/6fdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6fdr RCSB], [https://www.ebi.ac.uk/pdbsum/6fdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6fdr ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fd/6fdr_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=6fdr ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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==About this Structure==
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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>
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6FDR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii] with SF4 and F3S as [http://en.wikipedia.org/wiki/ligands ligands]. This structure superseeds the now removed PDB entry 1FDC. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=6FDR OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10387068 10387068]
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</div>
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[[Category: Azotobacter vinelandii]]
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<div class="pdbe-citations 6fdr" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Goodin, D.B.]]
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[[Category: Mcree, D.E.]]
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[[Category: Schipke, C.G.]]
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[[Category: Stout, C.D.]]
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[[Category: F3S]]
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[[Category: SF4]]
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[[Category: electron transport]]
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[[Category: iron-sulfur]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:32:34 2007''
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==See Also==
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*[[Ferredoxin 3D structures|Ferredoxin 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Azotobacter vinelandii]]
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[[Category: Large Structures]]
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[[Category: Goodin DB]]
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[[Category: Mcree DE]]
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[[Category: Schipke CG]]
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[[Category: Stout CD]]

Current revision

7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT 100K, NA DITHIONITE REDUCED AT PH 8.5, RESOLUTION 1.4 A

PDB ID 6fdr

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