1rdv: Difference between revisions

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{{Seed}}
[[Image:1rdv.png|left|200px]]


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==RUBREDOXIN FROM DESULFOVIBRIO VULGARIS MIYAZAKI F, TRIGONAL CRYSTAL FORM==
The line below this paragraph, containing "STRUCTURE_1rdv", creates the "Structure Box" on the page.
<StructureSection load='1rdv' size='340' side='right'caption='[[1rdv]], [[Resolution|resolution]] 2.00&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'>[[1rdv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._'Miyazaki_F' Desulfovibrio vulgaris str. 'Miyazaki F']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RDV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RDV 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]] 2&#8491;</td></tr>
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<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_1rdv|  PDB=1rdv  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rdv OCA], [https://pdbe.org/1rdv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rdv RCSB], [https://www.ebi.ac.uk/pdbsum/1rdv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rdv ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RUBR_DESVM RUBR_DESVM] 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/rd/1rdv_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=1rdv ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The structures of two crystal forms (form I, P3221, a = b = 43.7, c = 50.7 A; form II, P21, a = 27.3, b = 44.9, c = 51.2 A and beta = 90. 6 degrees ) of the rubredoxin from Desulfovibrio vulgaris Miyazaki F have been solved by the molecular-replacement method. Form I has been refined at a resolution of 2.0 A to an R value of 20.8% and includes 32 water molecules. Form II includes 86 water molecules and has been refined at 1.9 A resolution to an R value of 17.5%. In form II, there are three molecules in the asymmetric unit with the molecules related by a non-crystallographic 32 symmetry axis. In both crystal forms, it was found that only a few residues effectively participate in the formation of intermolecular contacts along both the crystallographic (form I) and the non-crystallographic (form II) 32 axes. The crystal structure of the form II crystal is compared with those of other rubredoxin molecules from anaerobic bacteria. From this comparison, a similarity in the core region, which is composed of aromatic residues and includes the active centre, has been revealed.


===RUBREDOXIN FROM DESULFOVIBRIO VULGARIS MIYAZAKI F, TRIGONAL CRYSTAL FORM===
Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki F in two crystal forms.,Misaki S, Morimoto Y, Ogata M, Yagi T, Higuchi Y, Yasuoka N Acta Crystallogr D Biol Crystallogr. 1999 Feb;55(Pt 2):408-13. PMID:10089348<ref>PMID:10089348</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1rdv" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_10089348}}, adds the Publication Abstract to the page
*[[Rubredoxin 3D structures|Rubredoxin 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 10089348 is the PubMed ID number.
*[[Rubredoxin PDB structures|Rubredoxin PDB structures]]
-->
== References ==
{{ABSTRACT_PUBMED_10089348}}
<references/>
 
__TOC__
==About this Structure==
</StructureSection>
1RDV is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RDV OCA].
[[Category: Desulfovibrio vulgaris str. 'Miyazaki F']]
 
[[Category: Large Structures]]
==Reference==
[[Category: Higuchi Y]]
<ref group="xtra">PMID:10089348</ref><references group="xtra"/>
[[Category: Yasuoka N]]
[[Category: Desulfovibrio vulgaris]]
[[Category: Higuchi, Y.]]
[[Category: Yasuoka, N.]]
[[Category: Electron transfer]]
[[Category: Iron-sulfur protein]]
[[Category: Metalloprotein]]
[[Category: Rubredoxin]]
[[Category: Sulfate-reducing bacterium]]
 
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Retrieved from "https://proteopedia.org/1rdv"