1gyo

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the di-tetraheme cytochrome c3 from Desulfovibrio gigas at 1.2 Angstrom resolution

Structural highlights

1gyo is a 2 chain structure with sequence from Megalodesulfovibrio gigas. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.2Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q9R638_MEGGA

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The structure of dimeric cytochrome c(3) from the sulfate-reducing bacterium Desulfovibrio gigas, diDg, obtained by ab initio methods was further refined to 1.2 A resolution, giving final reliability factors of R(free) = 14.8% and R = 12.4%. This cytochrome is a dimer of tetraheme cytochrome c(3) molecules covalently linked by two solvent-accessible disulfide bridges, a characteristic unique to members of the cytochrome c(3) superfamily. Anisotropic analysis using the semi-rigid TLS method shows different behaviour for analogous loops in each monomer arising from their different packing environments. A detailed sequence and structural comparison with all other known cytochrome c(3) domains in single- and multi-domain cytochromes c(3) shows the presence of structurally conserved regions in this family, despite the high variability of the amino-acid sequence. An internal water molecule is conserved in a common structural arrangement in all c(3) tetraheme domains, indicating a probable electron-transfer pathway between hemes I and II. Unique features of diDg are an internal methionine residue close to heme I and to one of the axial ligands of heme III, where all other structures of the cytochrome c(3) superfamily have a phenylalanine, and a rather unusual CXXXCH heme-binding motif only found so far in this cytochrome.

Structure of dimeric cytochrome c3 from Desulfovibrio gigas at 1.2 A resolution.,Aragao D, Frazao C, Sieker L, Sheldrick GM, LeGall J, Carrondo MA Acta Crystallogr D Biol Crystallogr. 2003 Apr;59(Pt 4):644-53. Epub 2003, Mar 25. PMID:12657783^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Aragao D, Frazao C, Sieker L, Sheldrick GM, LeGall J, Carrondo MA. Structure of dimeric cytochrome c3 from Desulfovibrio gigas at 1.2 A resolution. Acta Crystallogr D Biol Crystallogr. 2003 Apr;59(Pt 4):644-53. Epub 2003, Mar 25. PMID:12657783

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1gyo"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the di-tetraheme cytochrome c3 from Desulfovibrio gigas at 1.2 Angstrom resolution==
-<StructureSection load='1gyo' size='340' side='right' caption='[[1gyo]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
+<StructureSection load='1gyo' size='340' side='right'caption='[[1gyo]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1gyo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GYO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1gyo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Megalodesulfovibrio_gigas Megalodesulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GYO FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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]] 1.2&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyo OCA], [http://pdbe.org/1gyo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gyo RCSB], [http://www.ebi.ac.uk/pdbsum/1gyo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1gyo ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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=1gyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyo OCA], [https://pdbe.org/1gyo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gyo RCSB], [https://www.ebi.ac.uk/pdbsum/1gyo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gyo ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9R638_MEGGA Q9R638_MEGGA]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 12: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gy/1gyo_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 28: / Line 31: @@
 ==See Also==
-*[[Cytochrome c|Cytochrome c]]
+*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Desulfovibrio gigas]]
+[[Category: Large Structures]]
-[[Category: Aragao, D]]
+[[Category: Megalodesulfovibrio gigas]]
-[[Category: Carrondo, M A]]
+[[Category: Aragao D]]
-[[Category: Frazao, C]]
+[[Category: Carrondo MA]]
-[[Category: Legall, J]]
+[[Category: Frazao C]]
-[[Category: Sheldrick, G M]]
+[[Category: Legall J]]
-[[Category: Sieker, L]]
+[[Category: Sheldrick GM]]
-[[Category: Ab initio]]
+[[Category: Sieker L]]
-[[Category: Cytochrome c3]]
-[[Category: Di-tetraheme]]
-[[Category: Electron transfer]]
-[[Category: Electron transport]]

1gyo

From Proteopedia

Current revision

Crystal structure of the di-tetraheme cytochrome c3 from Desulfovibrio gigas at 1.2 Angstrom resolution

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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