7fd1

From Proteopedia

(Difference between revisions)

Revision as of 07:00, 4 April 2018

7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT PH 8.5, 100 K, 1.35 A

Structural highlights

7fd1 is a 1 chain structure with sequence from Azotobacter vinelandii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Schipke CG, Goodin DB, McRee DE, Stout CD. 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. Biochemistry. 1999 Jun 29;38(26):8228-39. PMID:10387068 doi:10.1021/bi983008i

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7fd1"

@@ Line 1: / Line 1: @@
 ==7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT PH 8.5, 100 K, 1.35 A==
 <StructureSection load='7fd1' size='340' side='right' caption='[[7fd1]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
@@ Line 4: / Line 5: @@
 <table><tr><td colspan='2'>[[7fd1]] is a 1 chain structure with 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=7FD1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7FD1 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7fd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fd1 OCA], [http://pdbe.org/7fd1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7fd1 RCSB], [http://www.ebi.ac.uk/pdbsum/7fd1 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7fd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fd1 OCA], [http://pdbe.org/7fd1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7fd1 RCSB], [http://www.ebi.ac.uk/pdbsum/7fd1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7fd1 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 12: / Line 13: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fd/7fd1_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fd/7fd1_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

7fd1

From Proteopedia

Revision as of 07:00, 4 April 2018

7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT PH 8.5, 100 K, 1.35 A

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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