2cym: Difference between revisions
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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== | ||
<StructureSection load='2cym' size='340' side='right'caption='[[2cym]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
You may | == Structural highlights == | ||
<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> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> | |||
<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> | |||
<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 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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2cym" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Cytochrome C 3D structures|Cytochrome C 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
== | |||
< | |||
[[Category: Desulfovibrio vulgaris]] | [[Category: Desulfovibrio vulgaris]] | ||
[[Category: Higuchi | [[Category: Large Structures]] | ||
[[Category: Morimoto | [[Category: Higuchi Y]] | ||
[[Category: Okumura | [[Category: Morimoto Y]] | ||
[[Category: Tani | [[Category: Okumura H]] | ||
[[Category: Yasuoka | [[Category: Tani T]] | ||
[[Category: Yasuoka N]] | |||
Latest revision as of 07:52, 13 August 2026
EFFECTS OF AMINO ACID SUBSTITUTION ON THREE-DIMENSIONAL STRUCTURE: AN X-RAY ANALYSIS OF CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 2 ANGSTROMS RESOLUTION
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