1cc5: Difference between revisions

From Proteopedia
Jump to navigationJump to search
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
New page: left|200px<br /><applet load="1cc5" size="450" color="white" frame="true" align="right" spinBox="true" caption="1cc5, resolution 2.5Å" /> '''CRYSTAL STRUCTURE OF ...
 
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
 
(17 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1cc5.gif|left|200px]]<br /><applet load="1cc5" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1cc5, resolution 2.5&Aring;" />
'''CRYSTAL STRUCTURE OF AZOTOBACTER CYTOCHROME C5 AT 2.5 ANGSTROMS RESOLUTION'''<br />


==Overview==
==CRYSTAL STRUCTURE OF AZOTOBACTER CYTOCHROME C5 AT 2.5 ANGSTROMS RESOLUTION==
The crystal structure of cytochrome c5 from Azotobacter vinelandii has, been solved and refined to an R value of 0.29 at 2.5 A resolution. The, structure of the oxidized protein was solved using a monoclinic crystal, form. The structure was solved by multiple isomorphous replacements, re-fit to a solvent-leveled multiple isomorphous replacement map, and, refined by restrained least squares. The structure reveals monomers, associated about the crystallographic 2-fold axis by hydrophobic contacts, at the "exposed heme edge". The overall conformation for the monomer is, similar to that of Pseudomonas aeruginosa cytochrome c551. However, relative to a common heme conformation, c5 and c551 differ by an average, of 6.8 A over 82 alpha-carbon positions and the propionates of c5 are much, more exposed to solvent. The shortest heme--heme contact at the "dimer", interface is 6.3 A (Fe to Fe 16.4 A). Alignment of c5 and c551 shows that, the two cytochromes, in spite of sequence differences, have remarkably, similar charge distributions. A disulfide stacks on a tyrosine between the, N- and C-terminal helices.
<StructureSection load='1cc5' size='340' side='right'caption='[[1cc5]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1cc5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CC5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CC5 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]] 2.5&#8491;</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=1cc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cc5 OCA], [https://pdbe.org/1cc5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cc5 RCSB], [https://www.ebi.ac.uk/pdbsum/1cc5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cc5 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CYC5_AZOVI CYC5_AZOVI]
== 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/cc/1cc5_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=1cc5 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of cytochrome c5 from Azotobacter vinelandii has been solved and refined to an R value of 0.29 at 2.5 A resolution. The structure of the oxidized protein was solved using a monoclinic crystal form. The structure was solved by multiple isomorphous replacements, re-fit to a solvent-leveled multiple isomorphous replacement map, and refined by restrained least squares. The structure reveals monomers associated about the crystallographic 2-fold axis by hydrophobic contacts at the "exposed heme edge". The overall conformation for the monomer is similar to that of Pseudomonas aeruginosa cytochrome c551. However, relative to a common heme conformation, c5 and c551 differ by an average of 6.8 A over 82 alpha-carbon positions and the propionates of c5 are much more exposed to solvent. The shortest heme--heme contact at the "dimer" interface is 6.3 A (Fe to Fe 16.4 A). Alignment of c5 and c551 shows that the two cytochromes, in spite of sequence differences, have remarkably similar charge distributions. A disulfide stacks on a tyrosine between the N- and C-terminal helices.


==About this Structure==
Crystal structure of Azotobacter cytochrome c5 at 2.5 A resolution.,Carter DC, Melis KA, O'Donnell SE, Burgess BK, Furey WR Jr, Wang BC, Stout CD J Mol Biol. 1985 Jul 20;184(2):279-95. PMID:2993632<ref>PMID:2993632</ref>
1CC5 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii] with HEM as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1CC5 OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Crystal structure of Azotobacter cytochrome c5 at 2.5 A resolution., Carter DC, Melis KA, O'Donnell SE, Burgess BK, Furey WR Jr, Wang BC, Stout CD, J Mol Biol. 1985 Jul 20;184(2):279-95. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2993632 2993632]
</div>
<div class="pdbe-citations 1cc5" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Azotobacter vinelandii]]
[[Category: Azotobacter vinelandii]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Carter, D.C.]]
[[Category: Carter DC]]
[[Category: Stout, C.D.]]
[[Category: Stout CD]]
[[Category: HEM]]
[[Category: electron transport (heme protein)]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 12:20:06 2007''
Retrieved from "https://proteopedia.org/1cc5"