2cym: Difference between revisions

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{{Seed}}
[[Image:2cym.png|left|200px]]


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==EFFECTS OF AMINO ACID SUBSTITUTION ON THREE-DIMENSIONAL STRUCTURE: AN X-RAY ANALYSIS OF CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 2 ANGSTROMS RESOLUTION==
The line below this paragraph, containing "STRUCTURE_2cym", creates the "Structure Box" on the page.
<StructureSection load='2cym' size='340' side='right'caption='[[2cym]], [[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'>[[2cym]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CYM 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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
{{STRUCTURE_2cym|  PDB=2cym  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cym OCA], [https://pdbe.org/2cym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cym RCSB], [https://www.ebi.ac.uk/pdbsum/2cym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cym ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CYC3_NITV2 CYC3_NITV2] Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.
== 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/cy/2cym_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=2cym ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The three-dimensional structure of cytochrome c3 from Desulfovibrio vulgaris Hildenborough has been determined by use of the molecular replacement method and refined at 2.0 A resolution. A suitable crystal of the cytochrome c3 was obtained from buffer solution (25 mM Tris-HCl, pH 7.4), with 75% ethanol as the precipitating reagent. Crystallographic data are as follows: a = 43.17 A, b = 62.91 A, c = 41.17 A, orthorhombic, P2(1)2(1)2(1) and Z = 4. Constrained least-squares refinement and a molecular dynamics procedure with a simulated structure annealing method yielded a crystallographic R-factor of 0.212. The similarity in the folding pattern of both cytochromes c3 is established, the mean deviation of the polypeptide backbone between the two structures being 0.367 A. Most of the amino acids substitutions from DvMF were located on the surface of the molecule, and in particular, S27 and V86 were placed near the propionic acid of the heme group so as to hang over the heme and the cleft of the molecule.


===EFFECTS OF AMINO ACID SUBSTITUTION ON THREE-DIMENSIONAL STRUCTURE: AN X-RAY ANALYSIS OF CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 2 ANGSTROMS RESOLUTION===
Effects of amino acid substitution on three-dimensional structure: an X-ray analysis of cytochrome c3 from Desulfovibrio vulgaris Hildenborough at 2 A resolution.,Morimoto Y, Tani T, Okumura H, Higuchi Y, Yasuoka N J Biochem. 1991 Oct;110(4):532-40. PMID:1663945<ref>PMID:1663945</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2cym" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_1663945}}, adds the Publication Abstract to the page
*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 1663945 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_1663945}}
__TOC__
 
</StructureSection>
==About this Structure==
2CYM is a [[Single protein]] 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=2CYM OCA].
 
==Reference==
Effects of amino acid substitution on three-dimensional structure: an X-ray analysis of cytochrome c3 from Desulfovibrio vulgaris Hildenborough at 2 A resolution., Morimoto Y, Tani T, Okumura H, Higuchi Y, Yasuoka N, J Biochem. 1991 Oct;110(4):532-40. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1663945 1663945]
[[Category: Desulfovibrio vulgaris]]
[[Category: Desulfovibrio vulgaris]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Higuchi, Y.]]
[[Category: Higuchi Y]]
[[Category: Morimoto, Y.]]
[[Category: Morimoto Y]]
[[Category: Okumura, H.]]
[[Category: Okumura H]]
[[Category: Tani, T.]]
[[Category: Tani T]]
[[Category: Yasuoka, N.]]
[[Category: Yasuoka N]]
[[Category: Electron transport]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 05:22:02 2008''
Retrieved from "https://proteopedia.org/2cym"