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New page: left|200px<br /><applet load="1fxd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1fxd, resolution 1.7Å" /> '''REFINED CRYSTAL STRUC...
 
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[[Image:1fxd.gif|left|200px]]<br /><applet load="1fxd" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1fxd, resolution 1.7&Aring;" />
'''REFINED CRYSTAL STRUCTURE OF FERREDOXIN II FROM DESULFOVIBRIO GIGAS AT 1.7 ANGSTROMS'''<br />


==Overview==
==REFINED CRYSTAL STRUCTURE OF FERREDOXIN II FROM DESULFOVIBRIO GIGAS AT 1.7 ANGSTROMS==
The crystal structure of ferredoxin II from Desulfovibrio gigas has been, determined using phasing from anomalous scattering data at a resolution of, 1.7 A and refined to an R-factor of 0.157. The molecule has an overall, chain fold similar to that of the other bacterial ferredoxins of known, structure. The molecule contains a single 3Fe-4S cluster with geometry, indistinguishable from the 4Fe-4S clusters, and a disulfide bond near the, site corresponding to the position of the second cluster of two-cluster, ferredoxins. The cluster is bound by cysteine residues 8, 14 and 50. The, side-chain of cysteine 11 extends away from the cluster, but could rotate, to become the fourth cysteine ligand in the four-iron form of the molecule, given a local adjustment of the polypeptide chain. This residue is, modified, however, by what appears to be a methanethiol group. There are a, total of eight NH . . . S bonds to the inorganic and cysteine sulfur atoms, of the Fe-S cluster. There is an additional residue found that is not, reported for the chemical sequence: according to the electron density a, valine residue should be inserted after residue 55.
<StructureSection load='1fxd' size='340' side='right'caption='[[1fxd]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1fxd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Megalodesulfovibrio_gigas Megalodesulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FXD FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SCH:S-METHYL-THIO-CYSTEINE'>SCH</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=1fxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fxd OCA], [https://pdbe.org/1fxd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fxd RCSB], [https://www.ebi.ac.uk/pdbsum/1fxd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fxd ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/FER_MEGGA FER_MEGGA] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.
== 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/fx/1fxd_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1fxd ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of ferredoxin II from Desulfovibrio gigas has been determined using phasing from anomalous scattering data at a resolution of 1.7 A and refined to an R-factor of 0.157. The molecule has an overall chain fold similar to that of the other bacterial ferredoxins of known structure. The molecule contains a single 3Fe-4S cluster with geometry indistinguishable from the 4Fe-4S clusters, and a disulfide bond near the site corresponding to the position of the second cluster of two-cluster ferredoxins. The cluster is bound by cysteine residues 8, 14 and 50. The side-chain of cysteine 11 extends away from the cluster, but could rotate to become the fourth cysteine ligand in the four-iron form of the molecule given a local adjustment of the polypeptide chain. This residue is modified, however, by what appears to be a methanethiol group. There are a total of eight NH . . . S bonds to the inorganic and cysteine sulfur atoms of the Fe-S cluster. There is an additional residue found that is not reported for the chemical sequence: according to the electron density a valine residue should be inserted after residue 55.


==About this Structure==
Refined crystal structure of ferredoxin II from Desulfovibrio gigas at 1.7 A.,Kissinger CR, Sieker LC, Adman ET, Jensen LH J Mol Biol. 1991 Jun 20;219(4):693-715. PMID:2056535<ref>PMID:2056535</ref>
1FXD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas] with F3S as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1FXD OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Refined crystal structure of ferredoxin II from Desulfovibrio gigas at 1.7 A., Kissinger CR, Sieker LC, Adman ET, Jensen LH, J Mol Biol. 1991 Jun 20;219(4):693-715. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2056535 2056535]
</div>
[[Category: Desulfovibrio gigas]]
<div class="pdbe-citations 1fxd" style="background-color:#fffaf0;"></div>
[[Category: Single protein]]
[[Category: Adman, E.T.]]
[[Category: Jensen, L.H.]]
[[Category: Kissinger, C.R.]]
[[Category: Sieker, L.C.]]
[[Category: F3S]]
[[Category: electron transfer(iron-sulfur)]]


''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:25:58 2007''
==See Also==
*[[Ferredoxin 3D structures|Ferredoxin 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Megalodesulfovibrio gigas]]
[[Category: Adman ET]]
[[Category: Jensen LH]]
[[Category: Kissinger CR]]
[[Category: Sieker LC]]
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