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6fd1

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7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII LOW TEMPERATURE, 1.35 A

Structural highlights

6fd1 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.
Method:	X-ray diffraction, Resolution 1.35Å
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 crystal structure of Azotobacter vinelandii ferredoxin I (FdI) at 100 K has been refined at 1.35 A resolution by full matrix block diagonal least-squares methods with anisotropic temperature factors for all non-hydrogen atoms and with hydrogen atoms included in the model. Fe-S bonds within the [3Fe-4S]+ and [4Fe-4S]2+ clusters of the protein are determined with an accuracy of at least 0.01 A. Analysis of metric parameters reveals greater variation in bonds and angles within the [3Fe-4S]+ cluster than in the [4Fe-4S]2+ cluster, whereas the opposite is true regarding the cysteine Sgamma atoms ligating to the two [Fe-S] cores. The [3Fe-4S]+ core is asymmetrically distorted by the protein matrix but relatively uniformly ligated by its three Cys ligands; in contrast the tetrahedral [4Fe-4S]2+ core is relatively symmetric but non-uniformily ligated by its four Cys ligands, three of which occur in a conserved CysxxCysxxCys residue motif. Comparison of the [3Fe-4S]+ clusters in FdI and Desulfovibrio gigas ferredoxin II, refined at 1.7 A resolution, indicates that within the limit of accuracy of the two refinements the cuboidal core is differently distorted in the two proteins. Comparison of the [3Fe-4S]+ core in FdI with the structure of a reduced [Fe3S4]o synthetic analog indicates that the protein-bound cluster displays distortions not intrinsic to the core itself. Nevertheless, both [3Fe-4S]+ and [Fe3S4]o cores have metric features consistent with expected trends due to net charge on Fe and valency of S, and both exhibit a splayed configuration with respect to their three mu2S atoms in the absence of a fourth Fe. Comparison of the [4Fe-4S]2+ cluster in FdI with the structures of [Fe4S4]2+ synthetic analogs shows that the protein bound and synthetic cubanes are very similar in geometric parameters, including the presence of tetragonal distortion in the FdI cluster common to this oxidation state.

Structure of Azotobacter vinelandii 7Fe ferredoxin at 1.35 A resolution and determination of the [Fe-S] bonds with 0.01 A accuracy.,Stout CD, Stura EA, McRee DE J Mol Biol. 1998 May 8;278(3):629-39. PMID:9600844^[1]

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

References

↑ Stout CD, Stura EA, McRee DE. Structure of Azotobacter vinelandii 7Fe ferredoxin at 1.35 A resolution and determination of the [Fe-S] bonds with 0.01 A accuracy. J Mol Biol. 1998 May 8;278(3):629-39. PMID:9600844 doi:S0022-2836(98)91732-6

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/6fd1"

Categories: Azotobacter vinelandii | Large Structures | Mcree DE | Stout CD | Stura EA

@@ Line 1: / Line 1: @@
 ==7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII LOW TEMPERATURE, 1.35 A==
-<StructureSection load='6fd1' size='340' side='right' caption='[[6fd1]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
+<StructureSection load='6fd1' size='340' side='right'caption='[[6fd1]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6fd1]] 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=6FD1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FD1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6fd1]] 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=6FD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6FD1 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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.35&#8491;</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=6fd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fd1 OCA], [http://pdbe.org/6fd1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fd1 RCSB], [http://www.ebi.ac.uk/pdbsum/6fd1 PDBsum]</span></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>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6fd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fd1 OCA], [https://pdbe.org/6fd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6fd1 RCSB], [https://www.ebi.ac.uk/pdbsum/6fd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6fd1 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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.
+[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/6fd1_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fd/6fd1_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 31: @@
 ==See Also==
-*[[Ferredoxin|Ferredoxin]]
+*[[Ferredoxin 3D structures|Ferredoxin 3D structures]]
 == References ==
 <references/>
@@ Line 35: / Line 37: @@
 </StructureSection>
 [[Category: Azotobacter vinelandii]]
-[[Category: Mcree, D E]]
+[[Category: Large Structures]]
-[[Category: Stout, C D]]
+[[Category: Mcree DE]]
-[[Category: Stura, E A]]
+[[Category: Stout CD]]
-[[Category: Electron transport]]
+[[Category: Stura EA]]
-[[Category: Iron-sulfur]]

6fd1

From Proteopedia

Current revision

7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII LOW TEMPERATURE, 1.35 A

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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