1rmv
From Proteopedia
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|PDB= 1rmv |SIZE=350|CAPTION= <scene name='initialview01'>1rmv</scene>, resolution 2.9Å | |PDB= 1rmv |SIZE=350|CAPTION= <scene name='initialview01'>1rmv</scene>, resolution 2.9Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=ACE:ACETYL GROUP'>ACE</scene> | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmv OCA], [http://www.ebi.ac.uk/pdbsum/1rmv PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rmv RCSB]</span> | ||
}} | }} | ||
| Line 24: | Line 27: | ||
[[Category: Stubbs, G.]] | [[Category: Stubbs, G.]] | ||
[[Category: Wang, H.]] | [[Category: Wang, H.]] | ||
| - | [[Category: ACE]] | ||
[[Category: coat protein (viral)]] | [[Category: coat protein (viral)]] | ||
[[Category: complex (coat protein/rna)]] | [[Category: complex (coat protein/rna)]] | ||
| Line 32: | Line 34: | ||
[[Category: tobamovirus]] | [[Category: tobamovirus]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:30:18 2008'' |
Revision as of 20:30, 30 March 2008
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| , resolution 2.9Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
RIBGRASS MOSAIC VIRUS, FIBER DIFFRACTION
Overview
The molecular dynamics (MD) method has been adapted for refinement of the structures of helical macromolecular aggregates aginst X-ray fiber diffraction data. To test the effectiveness of the method, refinements of the tobacco mosaic virus structure were carried out against a set of simulated fiber diffraction intensities using the MD method as well as the conventional restrained least-squares (RLS) method. The MD refinement converged to a very low R factor and produced a structure with generally satisfactory sterochemistry, while the RLS refinemnt was trapped at a local energy minimum with a larger R factor. Results suggest that the effective experimental radius of convergence of the MD method is significantly greater than that of the RLS method. Even when the initial structure is too far from the true structure to allow direct refinement, the MD method is able to find local minima that resemble the true structure sufficiently to allow improved phasing and thus lead to interpretable difference maps for model rebuilding.
About this Structure
1RMV is a Single protein structure of sequence from Ribgrass mosaic virus. Full crystallographic information is available from OCA.
Reference
Molecular dynamics in refinement against fiber diffraction data., Wang H, Stubbs G, Acta Crystallogr A. 1993 May 1;49(3):504-13. PMID:8129880
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