1s05: Difference between revisions
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'''NMR-validated structural model for oxidized R.palustris cytochrome c556'''<br /> | '''NMR-validated structural model for oxidized R.palustris cytochrome c556'''<br /> | ||
==Overview== | ==Overview== | ||
The structure of oxidized Rhodopseudomonas palustris cytochrome c(556) has | The structure of oxidized Rhodopseudomonas palustris cytochrome c(556) has been modeled after that of high-spin cytochrome c' from the same bacterium, the latter being the protein with the greatest sequence identity (35%) among all sequenced proteins in the genomes. The two proteins differ in the number of ligands to iron and in spin state, the former being six-coordinate low-spin and the latter five-coordinate high-spin. In order to validate this modeled structure, several structural restraints were obtained by performing a restricted set of NMR experiments, without performing a complete assignment of the protein signals. The aim was to exploit the special restraints arising from the paramagnetism of the metal ion. A total of 43 residual-dipolar-coupling and 74 pseudocontact-shift restraints, which together sampled all regions of the protein, were used in conjunction with over 40 routinely obtained NOE distance restraints. A calculation procedure was undertaken combining the program MODELLER and the solution structure determination program PARAMAGNETIC DYANA, which includes paramagnetism-based restraints. The directions and magnitude of the magnetic susceptibility anisotropy tensor were also calculated. The approach readily provides useful results, especially for paramagnetic metalloproteins of moderate to large dimensions. | ||
==About this Structure== | ==About this Structure== | ||
1S05 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rhodopseudomonas_palustris Rhodopseudomonas palustris] with HEM as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | 1S05 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rhodopseudomonas_palustris Rhodopseudomonas palustris] 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=1S05 OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Bertini, I.]] | [[Category: Bertini, I.]] | ||
[[Category: Faraone-Mennella, J.]] | [[Category: Faraone-Mennella, J.]] | ||
[[Category: Gray, H | [[Category: Gray, H B.]] | ||
[[Category: Luchinat, C.]] | [[Category: Luchinat, C.]] | ||
[[Category: Parigi, G.]] | [[Category: Parigi, G.]] | ||
[[Category: Winkler, J | [[Category: Winkler, J R.]] | ||
[[Category: HEM]] | [[Category: HEM]] | ||
[[Category: this is a model obtained by nmr-restrained modeling and minimization.]] | [[Category: this is a model obtained by nmr-restrained modeling and minimization.]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:56:28 2008'' | ||
Revision as of 15:56, 21 February 2008
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NMR-validated structural model for oxidized R.palustris cytochrome c556
OverviewOverview
The structure of oxidized Rhodopseudomonas palustris cytochrome c(556) has been modeled after that of high-spin cytochrome c' from the same bacterium, the latter being the protein with the greatest sequence identity (35%) among all sequenced proteins in the genomes. The two proteins differ in the number of ligands to iron and in spin state, the former being six-coordinate low-spin and the latter five-coordinate high-spin. In order to validate this modeled structure, several structural restraints were obtained by performing a restricted set of NMR experiments, without performing a complete assignment of the protein signals. The aim was to exploit the special restraints arising from the paramagnetism of the metal ion. A total of 43 residual-dipolar-coupling and 74 pseudocontact-shift restraints, which together sampled all regions of the protein, were used in conjunction with over 40 routinely obtained NOE distance restraints. A calculation procedure was undertaken combining the program MODELLER and the solution structure determination program PARAMAGNETIC DYANA, which includes paramagnetism-based restraints. The directions and magnitude of the magnetic susceptibility anisotropy tensor were also calculated. The approach readily provides useful results, especially for paramagnetic metalloproteins of moderate to large dimensions.
About this StructureAbout this Structure
1S05 is a Single protein structure of sequence from Rhodopseudomonas palustris with as ligand. Full crystallographic information is available from OCA.
ReferenceReference
NMR-validated structural model for oxidized Rhodopseudomonas palustris cytochrome c(556)., Bertini I, Faraone-Mennella J, Gray HB, Luchinat C, Parigi G, Winkler JR, J Biol Inorg Chem. 2004 Mar;9(2):224-30. Epub 2004 Jan 20. PMID:14735333
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