2dvh

From Proteopedia

(Difference between revisions)

Revision as of 11:38, 10 February 2021

THE Y64A MUTANT OF CYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH, NMR, 39 STRUCTURES

Structural highlights

2dvh is a 1 chain structure with sequence from Desvh. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	M13CYF (DESVH)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[CY553_DESVH] Natural electron acceptor for a formate dehydrogenase.

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 solution structure of Desulfovibrio vulgaris Hildenborough (DvH) ferrocytochrome c553 has been determined by nuclear magnetic resonance spectroscopy and combined simulated annealing/high temperature restrained molecular dynamics calculations. This three-stage protocol consists of an initial determination of overall fold from randomised co-ordinates, followed by a 20 picosecond exploratory stage, during which the non-bonded terms are simplified to facilitate as broad a sampling of conformational space as possible, and a 26 picosecond refinement stage, using the full AMBER force field. This latter stage systematically improved the energetic and convergence characteristics of the ensemble, while still satisfying the experimental restraints. Forty structures have been obtained from a total of 875 distance constraints for this protein of 79 amino acid residues. The root-mean-square deviation over all residues with respect to the mean is 0.70(+/- 0.12)A for the backbone (N, C alpha and C') atoms. Two conformations of the turn motif at the solvent/heme cleft interface have been identified, both fulfilling the experimental data and having equally viable energetic characteristics. The stability of the ensemble and the dynamic characteristics have been further investigated by subjecting ten of the structures to constraint-free molecular dynamics calculations (130 picoseconds) in vacuo. The structures were found to be stable to within 1.5 A of the initial backbone conformation. Comparison with the dynamic behaviour of the restrained molecular dynamics calculations has been used to identify regions of inherent flexibility in the molecule.

Structure and dynamics of ferrocytochrome c553 from Desulfovibrio vulgaris studied by NMR spectroscopy and restrained molecular dynamics.,Blackledge MJ, Medvedeva S, Poncin M, Guerlesquin F, Bruschi M, Marion D J Mol Biol. 1995 Feb 3;245(5):661-81. PMID:7844834^[1]

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

References

↑ Blackledge MJ, Medvedeva S, Poncin M, Guerlesquin F, Bruschi M, Marion D. Structure and dynamics of ferrocytochrome c553 from Desulfovibrio vulgaris studied by NMR spectroscopy and restrained molecular dynamics. J Mol Biol. 1995 Feb 3;245(5):661-81. PMID:7844834 doi:http://dx.doi.org/10.1006/jmbi.1994.0054

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/2dvh"

@@ Line 1: / Line 1: @@
 ==THE Y64A MUTANT OF CYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH, NMR, 39 STRUCTURES==
-<StructureSection load='2dvh' size='340' side='right' caption='[[2dvh]], [[NMR_Ensembles_of_Models | 39 NMR models]]' scene=''>
+<StructureSection load='2dvh' size='340' side='right'caption='[[2dvh]], [[NMR_Ensembles_of_Models | 39 NMR models]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2dvh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desvh Desvh]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DVH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DVH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2dvh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desvh Desvh]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DVH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DVH FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene></td></tr>
+</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">M13CYF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 DESVH])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">M13CYF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 DESVH])</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=2dvh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dvh OCA], [http://pdbe.org/2dvh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dvh RCSB], [http://www.ebi.ac.uk/pdbsum/2dvh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dvh 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=2dvh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dvh OCA], [https://pdbe.org/2dvh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dvh RCSB], [https://www.ebi.ac.uk/pdbsum/2dvh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dvh ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CY553_DESVH CY553_DESVH]] Natural electron acceptor for a formate dehydrogenase.
+[[https://www.uniprot.org/uniprot/CY553_DESVH CY553_DESVH]] Natural electron acceptor for a formate dehydrogenase.
 == 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/dv/2dvh_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dv/2dvh_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 29: @@
 </div>
 <div class="pdbe-citations 2dvh" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
 == References ==
 <references/>
@@ Line 34: / Line 37: @@
 </StructureSection>
 [[Category: Desvh]]
+[[Category: Large Structures]]
 [[Category: Blackledge, M J]]
 [[Category: Dolla, A]]

2dvh

From Proteopedia

Revision as of 11:38, 10 February 2021

THE Y64A MUTANT OF CYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH, NMR, 39 STRUCTURES

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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