5fd1: Difference between revisions

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<StructureSection load='5fd1' size='340' side='right'caption='[[5fd1]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='5fd1' size='340' side='right'caption='[[5fd1]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5fd1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_478 Atcc 478]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fd1 4fd1], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3fd1 3fd1], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2fd1 2fd1] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fd1 1fd1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FD1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FD1 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5fd1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fd1 4fd1], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3fd1 3fd1], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2fd1 2fd1] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fd1 1fd1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FD1 FirstGlance]. <br>
</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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4fd1|4fd1]], [[1fda|1fda]], [[1fdb|1fdb]], [[1fdc|1fdc]]</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'>[http://proteopedia.org/fgij/fg.htm?mol=5fd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fd1 OCA], [http://pdbe.org/5fd1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fd1 RCSB], [http://www.ebi.ac.uk/pdbsum/5fd1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fd1 ProSAT]</span></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=5fd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fd1 OCA], [https://pdbe.org/5fd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fd1 RCSB], [https://www.ebi.ac.uk/pdbsum/5fd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fd1 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== 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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=5fd1 ConSurf].
</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=5fd1 ConSurf].
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<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Crystal structures of Azotobacter vinelandii ferredoxin I (FdI) have been solved and refined at 2.2 to 1.9-A resolution at pH 8 and 6 for both the oxidized and dithionite-reduced proteins. Only the [3Fe-4S] cluster is reduced by dithionite. The four structures (denoted FdI8ox, FdI8red, FdI6ox, and FdI6red) have been compared to address three questions: the effect of reduction at pH 8, the effect of pH change on the structure, and the effect of reduction at pH 6. Comparison of the FdI8ox and FdI8red structures shows that Asp-15 changes conformation in a manner consistent with increased anionic repulsion between this residue and the reduced [3Fe-4S]0 cluster. By revealing an electrostatic interaction between Asp-15 and the [3Fe-4S] cluster, this result supports the conclusion in the accompanying paper (Shen, B., Martin, L. L., Butt, J. N., Armstrong, F. A., Stout, C. D., Jensen, G. M., Stephens, P. J., LaMar, G. N., Gorst, C. M., and Burgess, B. K. (1993) J. Biol. Chem. 268, 25928-25939) that Asp-15 participates in protonation of the reduced [3Fe-4S]0 cluster at acid pH. The [3Fe-4S]0 cluster in the FdI8red structure also displays a distinct shift within the protein as well as internal distortions when compared to the [3Fe-4S]+ cluster in the FdI8ox structure. Comparison of the FdI8ox and FdI6ox structures shows that pH change does not have any significant effect on the [3Fe-4S]+ cluster or surrounding residues. Comparison of the FdI6ox and FdI6red structures shows that reduction at pH 6 also does not have any significant effect on the [3Fe-4S] cluster or Asp-15. The absence of structural change supports the conclusion that at acid pH, the reduced [3Fe-4S] cluster is protonated, i.e. [3Fe-4S]0-H+ (Shen et al., 1993). The cluster is not shifted or distorted as in the FdI8red structure. Instead, the [3Fe-4S]o-H+ cluster FdI8red is structurally similar to the [3Fe-4S]+ cluster (FdI8ox, FdI6ox), which has the same net charge. An Asp-15-Lys-84 salt bridge is observed in all four structures, indicating that Asp-15 is ionized at pH 8 and 6. An ionized state for Asp-15 is also implied by a lack of conformational change in Lys-84; the side chain of this residue rearranges when Asp-15 is substituted with a neutral amino acid (Shen et al., 1993).(ABSTRACT TRUNCATED AT 400 WORDS)
Crystal structures of oxidized and reduced Azotobacter vinelandii ferredoxin at pH 8 and 6.,Stout CD J Biol Chem. 1993 Dec 5;268(34):25920-7. PMID:8245025<ref>PMID:8245025</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5fd1" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ferredoxin 3D structures|Ferredoxin 3D structures]]
*[[Ferredoxin 3D structures|Ferredoxin 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 478]]
[[Category: Azotobacter vinelandii]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Stout, C D]]
[[Category: Stout CD]]

Latest revision as of 17:08, 13 March 2024

CRYSTAL STRUCTURES OF OXIDIZED AND REDUCED AZOTOBACTER VINELANDII FERREDOXIN AT PH 8 AND PH 6CRYSTAL STRUCTURES OF OXIDIZED AND REDUCED AZOTOBACTER VINELANDII FERREDOXIN AT PH 8 AND PH 6

Structural highlights

5fd1 is a 1 chain structure with sequence from Azotobacter vinelandii. This structure supersedes the now removed PDB entries 4fd1, 3fd1, 2fd1 and 1fd1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
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.

See Also

5fd1, resolution 1.90Å

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