1dvh: Difference between revisions

Revision as of 11:45, 20 March 2008

Ligands:

Coordinates:

STRUCTURE AND DYNAMICS OF FERROCYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS STUDIED BY NMR SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS

OverviewOverview

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.

About this StructureAbout this Structure

1DVH is a Single protein structure of sequence from Desulfovibrio vulgaris. Full crystallographic information is available from OCA.

ReferenceReference

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

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OCA

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-[[Image:1dvh.jpg|left|200px]]<br /><applet load="1dvh" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:1dvh.jpg|left|200px]]
-caption="1dvh" />
-'''STRUCTURE AND DYNAMICS OF FERROCYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS STUDIED BY NMR SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS'''<br />
+ {{Structure
+|PDB= 1dvh |SIZE=350|CAPTION= <scene name='initialview01'>1dvh</scene>
+|SITE=
+|LIGAND= <scene name='pdbligand=HEM:PROTOPORPHYRIN IX CONTAINING FE'>HEM</scene>
+|ACTIVITY=
+|GENE=
+}}
+'''STRUCTURE AND DYNAMICS OF FERROCYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS STUDIED BY NMR SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-DVH is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris] with <scene name='pdbligand=HEM:'>HEM</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DVH OCA].
+DVH is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DVH OCA].
 ==Reference==
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7844834 7844834]
+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:[http://www.ncbi.nlm.nih.gov/pubmed/7844834 7844834]
 [[Category: Desulfovibrio vulgaris]]
 [[Category: Single protein]]
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 [[Category: electron transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:20:53 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:45:05 2008''