1fxd: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(14 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1fxd.gif|left|200px]]


<!--
==REFINED CRYSTAL STRUCTURE OF FERREDOXIN II FROM DESULFOVIBRIO GIGAS AT 1.7 ANGSTROMS==
The line below this paragraph, containing "STRUCTURE_1fxd", creates the "Structure Box" on the page.
<StructureSection load='1fxd' size='340' side='right'caption='[[1fxd]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</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=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=SCH:S-METHYL-THIO-CYSTEINE'>SCH</scene></td></tr>
{{STRUCTURE_1fxd|  PDB=1fxd |  SCENE= }}
<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/initialview01.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>


'''REFINED CRYSTAL STRUCTURE OF FERREDOXIN II FROM DESULFOVIBRIO GIGAS AT 1.7 ANGSTROMS'''
==See Also==
 
*[[Ferredoxin 3D structures|Ferredoxin 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
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.
[[Category: Large Structures]]
 
[[Category: Megalodesulfovibrio gigas]]
==About this Structure==
[[Category: Adman ET]]
1FXD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FXD OCA].
[[Category: Jensen LH]]
 
[[Category: Kissinger CR]]
==Reference==
[[Category: Sieker LC]]
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://www.ncbi.nlm.nih.gov/pubmed/2056535 2056535]
[[Category: Desulfovibrio gigas]]
[[Category: Single protein]]
[[Category: Adman, E T.]]
[[Category: Jensen, L H.]]
[[Category: Kissinger, C R.]]
[[Category: Sieker, L C.]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 16:52:19 2008''

Latest revision as of 14:17, 27 March 2024

REFINED CRYSTAL STRUCTURE OF FERREDOXIN II FROM DESULFOVIBRIO GIGAS AT 1.7 ANGSTROMSREFINED CRYSTAL STRUCTURE OF FERREDOXIN II FROM DESULFOVIBRIO GIGAS AT 1.7 ANGSTROMS

Structural highlights

1fxd is a 1 chain structure with sequence from Megalodesulfovibrio gigas. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.7Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FER_MEGGA Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.

Evolutionary Conservation

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

See Also

1fxd, resolution 1.70Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1fxd&oldid=4114076"