2dsx: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(11 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2dsx.gif|left|200px]]


<!--
==Crystal structure of rubredoxin from Desulfovibrio gigas to ultra-high 0.68 A resolution==
The line below this paragraph, containing "STRUCTURE_2dsx", creates the "Structure Box" on the page.
<StructureSection load='2dsx' size='340' side='right'caption='[[2dsx]], [[Resolution|resolution]] 0.68&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'>[[2dsx]] 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=2DSX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DSX 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]] 0.68&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
{{STRUCTURE_2dsx| PDB=2dsx |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dsx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dsx OCA], [https://pdbe.org/2dsx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dsx RCSB], [https://www.ebi.ac.uk/pdbsum/2dsx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dsx ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RUBR_MEGGA RUBR_MEGGA] Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule.  Electron acceptor for cytoplasmic lactate dehydrogenase.
== 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/ds/2dsx_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=2dsx ConSurf].
<div style="clear:both"></div>


'''Crystal structure of rubredoxin from Desulfovibrio gigas to ultra-high 0.68 A resolution'''
==See Also==
 
*[[Rubredoxin 3D structures|Rubredoxin 3D structures]]
 
*[[Rubredoxin PDB structures|Rubredoxin PDB structures]]
==Overview==
__TOC__
Rubredoxin (D.g. Rd) is a small non-heme iron-sulfur protein shown to function as a redox coupling protein from the sulfate reducing bacteria Desulfovibrio gigas. The protein is generally purified from anaerobic bacteria in which it is thought to be involved in electron transfer or exchange processes. Rd transfers an electron to oxygen to form water as part of a unique electron transfer chain, composed by NADH:rubredoxin oxidoreductase (NRO), rubredoxin and rubredoxin:oxygen oxidoreductase (ROO) in D.g. The crystal structure of D.g. Rd has been determined by means of both a Fe single-wavelength anomalous dispersion (SAD) signal and the direct method, and refined to an ultra-high 0.68 A resolution, using X-ray from a synchrotron. Rd contains one iron atom bound in a tetrahedral coordination by the sulfur atoms of four cysteinyl residues. Hydrophobic and pi-pi interactions maintain the internal Rd folding. Multiple conformations of the iron-sulfur cluster and amino acid residues are observed and indicate its unique mechanism of electron transfer. Several hydrogen bonds, including N-H...SG of the iron-sulfur, are revealed clearly in maps of electron density. Abundant waters bound to C-O peptides of residues Val8, Cys9, Gly10, Ala38, and Gly43, which may be involved in electron transfer. This ultrahigh-resolution structure allows us to study in great detail the relationship between structure and function of rubredoxin, such as salt bridges, hydrogen bonds, water structures, cysteine ligands, iron-sulfur cluster, and distributions of electron density among activity sites. For the first time, this information will provide a clear role for this protein in a strict anaerobic bacterium.
</StructureSection>
 
[[Category: Large Structures]]
==About this Structure==
[[Category: Megalodesulfovibrio gigas]]
2DSX 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=2DSX OCA].
[[Category: Chen C-J]]
 
[[Category: Huang Y-C]]
==Reference==
[[Category: Lin Y-H]]
Crystal structure of rubredoxin from Desulfovibrio gigas to ultra-high 0.68 A resolution., Chen CJ, Lin YH, Huang YC, Liu MY, Biochem Biophys Res Commun. 2006 Oct 13;349(1):79-90. Epub 2006 Aug 11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16930541 16930541]
[[Category: Liu M-Y]]
[[Category: Desulfovibrio gigas]]
[[Category: Single protein]]
[[Category: Chen, C J.]]
[[Category: Huang, Y C.]]
[[Category: Lin, Y H.]]
[[Category: Liu, M Y.]]
[[Category: Desulfovibrio giga]]
[[Category: Redox]]
[[Category: Rubredoxin]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 01:13:50 2008''

Latest revision as of 16:48, 13 March 2024

Crystal structure of rubredoxin from Desulfovibrio gigas to ultra-high 0.68 A resolutionCrystal structure of rubredoxin from Desulfovibrio gigas to ultra-high 0.68 A resolution

Structural highlights

2dsx 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 0.68Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RUBR_MEGGA Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule. Electron acceptor for cytoplasmic lactate dehydrogenase.

Evolutionary Conservation

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

See Also

2dsx, resolution 0.68Å

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=2dsx&oldid=4088731"