1dvh: Difference between revisions
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< | ==STRUCTURE AND DYNAMICS OF FERROCYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS STUDIED BY NMR SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS== | ||
<StructureSection load='1dvh' size='340' side='right'caption='[[1dvh]]' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1dvh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DVH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DVH FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 36 models</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=1dvh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dvh OCA], [https://pdbe.org/1dvh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dvh RCSB], [https://www.ebi.ac.uk/pdbsum/1dvh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dvh ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/CY553_NITV2 CY553_NITV2] 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/1dvh_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</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=1dvh ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:7844834</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1dvh" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Cytochrome C 3D structures|Cytochrome C 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
== | |||
< | |||
[[Category: Desulfovibrio vulgaris]] | [[Category: Desulfovibrio vulgaris]] | ||
[[Category: Blackledge | [[Category: Large Structures]] | ||
[[Category: Bruschi | [[Category: Blackledge MJ]] | ||
[[Category: Guerlesquin | [[Category: Bruschi M]] | ||
[[Category: Marion | [[Category: Guerlesquin F]] | ||
[[Category: Medvedeva | [[Category: Marion D]] | ||
[[Category: Poncin | [[Category: Medvedeva S]] | ||
[[Category: Poncin M]] | |||
Latest revision as of 09:33, 30 October 2024
STRUCTURE AND DYNAMICS OF FERROCYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS STUDIED BY NMR SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICSSTRUCTURE AND DYNAMICS OF FERROCYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS STUDIED BY NMR SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS
Structural highlights
FunctionCY553_NITV2 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 PubMedThe 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. See AlsoReferences
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