2bgv: Difference between revisions

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<StructureSection load='2bgv' size='340' side='right'caption='[[2bgv]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='2bgv' size='340' side='right'caption='[[2bgv]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2bgv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_25364 Atcc 25364]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BGV FirstGlance]. <br>
<table><tr><td colspan='2'>[[2bgv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_versutus Paracoccus versutus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BGV FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2bh4|2bh4]], [[2bh5|2bh5]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</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=2bgv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bgv OCA], [https://pdbe.org/2bgv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bgv RCSB], [https://www.ebi.ac.uk/pdbsum/2bgv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bgv ProSAT]</span></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=2bgv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bgv OCA], [https://pdbe.org/2bgv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bgv RCSB], [https://www.ebi.ac.uk/pdbsum/2bgv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bgv ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CY550_PARVE CY550_PARVE]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=2bgv ConSurf].
</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=2bgv ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The structure of cytochrome c-550 from the nonphotosynthetic bacteria Paraccocus versutus has been solved by X-ray crystallography to 1.90 A resolution, and reveals a high structural homology to other bacterial cytochromes c(2). The effect of replacing the axial heme-iron methionine ligand with a lysine residue on protein structure and unfolding has been assessed using the M100K variant. From X-ray structures at 1.95 and 1.55 A resolution it became clear that the amino group of the lysine side chain coordinates to the heme-iron. Structural differences compared to the wild-type protein are confined to the lysine ligand loop connecting helices four and five. In the heme cavity an additional water molecule is found which participates in an H-bonding interaction with the lysine ligand. Under cryo-conditions extra electron density in the lysine ligand loop is revealed, leading to residues K97 to T101 being modeled with a double main-chain conformation. Upon unfolding, dissociation of the lysine ligand from the heme-iron is shown to be pH dependent, with NMR data consistent with the occurrence of a ligand exchange mechanism similar to that seen for the wild-type protein.
The effect of replacing the axial methionine ligand with a lysine residue in cytochrome c-550 from Paracoccus versutus assessed by X-ray crystallography and unfolding.,Worrall JA, van Roon AM, Ubbink M, Canters GW FEBS J. 2005 May;272(10):2441-55. PMID:15885094<ref>PMID:15885094</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2bgv" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 25364]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Canters, G W]]
[[Category: Paracoccus versutus]]
[[Category: Roon, A M.M Van]]
[[Category: Canters GW]]
[[Category: Ubbink, M]]
[[Category: Ubbink M]]
[[Category: Worrall, J A.R]]
[[Category: Van Roon A-MM]]
[[Category: C-type cytochrome]]
[[Category: Worrall JAR]]
[[Category: Electron transfer]]
[[Category: Heme group]]
[[Category: Pyrrolidone carboxylic acid]]

Revision as of 06:37, 1 May 2024

X-ray structure of ferric cytochrome c-550 from Paracoccus versutus

2bgv, resolution 1.90Å

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