2dvh
From Proteopedia
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| - | [[Image:2dvh.gif|left|200px]]< | + | [[Image:2dvh.gif|left|200px]] |
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| - | '''THE Y64A MUTANT OF CYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH, NMR, 39 STRUCTURES''' | + | {{Structure |
| + | |PDB= 2dvh |SIZE=350|CAPTION= <scene name='initialview01'>2dvh</scene> | ||
| + | |SITE= <scene name='pdbsite=HEC:Hem+Binding+Site'>HEC</scene> | ||
| + | |LIGAND= <scene name='pdbligand=HEC:HEME C'>HEC</scene> | ||
| + | |ACTIVITY= | ||
| + | |GENE= M13CYF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=881 Desulfovibrio vulgaris]) | ||
| + | }} | ||
| + | |||
| + | '''THE Y64A MUTANT OF CYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH, NMR, 39 STRUCTURES''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2DVH is a [ | + | 2DVH 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=2DVH OCA]. |
==Reference== | ==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:// | + | 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: Desulfovibrio vulgaris]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: heme]] | [[Category: heme]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:32:02 2008'' |
Revision as of 14:32, 20 March 2008
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| Sites: | |||||||
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| Gene: | M13CYF (Desulfovibrio vulgaris) | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
THE Y64A MUTANT OF CYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH, NMR, 39 STRUCTURES
Overview
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 Structure
2DVH is a Single protein structure of sequence from Desulfovibrio vulgaris. Full crystallographic information is available from 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:7844834
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