7fdr: Difference between revisions

Revision as of 20:17, 21 February 2008

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

OverviewOverview

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.

About this StructureAbout this Structure

7FDR is a Single protein structure of sequence from Azotobacter vinelandii with and as ligands. Full crystallographic information is available from OCA.

ReferenceReference

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

Page seeded by OCA on Thu Feb 21 19:17:06 2008

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OCA

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-[[Image:7fdr.gif|left|200px]]<br /><applet load="7fdr" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:7fdr.gif|left|200px]]<br /><applet load="7fdr" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="7fdr, resolution 1.4&Aring;" />
 '''7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII, NA DITHIONITE REDUCED, PH 8.5, 1.4A RESOLUTION, 100 K'''<br />
 ==Overview==
-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.
+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.
 ==About this Structure==
-FDR 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]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=7FDR OCA].
+FDR 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 <scene name='pdbligand=SF4:'>SF4</scene> and <scene name='pdbligand=F3S:'>F3S</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FDR OCA].
 ==Reference==
@@ Line 13: / Line 13: @@
 [[Category: Azotobacter vinelandii]]
 [[Category: Single protein]]
-[[Category: Goodin, D.B.]]
+[[Category: Goodin, D B.]]
-[[Category: Mcree, D.E.]]
+[[Category: Mcree, D E.]]
-[[Category: Schipke, C.G.]]
+[[Category: Schipke, C G.]]
-[[Category: Stout, C.D.]]
+[[Category: Stout, C D.]]
 [[Category: F3S]]
 [[Category: SF4]]
@@ Line 22: / Line 22: @@
 [[Category: iron-sulfur]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:21:05 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:17:06 2008''