1vcx
From Proteopedia
(New page: 200px<br /><applet load="1vcx" size="450" color="white" frame="true" align="right" spinBox="true" caption="1vcx, resolution 1.50Å" /> '''Neutron Crystal Stru...) |
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| - | [[Image:1vcx.gif|left|200px]]<br /><applet load="1vcx" size=" | + | [[Image:1vcx.gif|left|200px]]<br /><applet load="1vcx" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1vcx, resolution 1.50Å" /> | caption="1vcx, resolution 1.50Å" /> | ||
'''Neutron Crystal Structure of the Wild Type Rubredoxin from Pyrococcus Furiosus at 1.5A Resolution'''<br /> | '''Neutron Crystal Structure of the Wild Type Rubredoxin from Pyrococcus Furiosus at 1.5A Resolution'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The structure of a partially deuterated rubredoxin from the | + | The structure of a partially deuterated rubredoxin from the hyperthermophilic archaeon Pyrococcus furiosus, an organism that grows optimally at 100 degrees C, was determined by using the neutron single-crystal diffractometer dedicated for biological macromolecules (BIX-3) at the JRR-3M reactor of the Japan Atomic Energy Research Institute. Data were collected at room temperature up to a resolution of 1.5 A, and the completeness factor of the data set was 81.9%. The model contains 306 H and 50 D atoms. A total of 37 hydration water molecules were identified, with 15 having all three atoms fully located and the remaining D2O molecules partially defined. The model has been refined to final agreement factors of R = 18.6% and Rfree = 21.7%. Several orientations of the O-D bonds of side chains, whose assignments from x-ray data were previously ambiguous, were clearly visible in the neutron structure. Although most backbone N-H bonds had undergone some degree of H/D exchange throughout the rubredoxin molecule, 5 H atom positions still had distinctly negative (H) peaks. The neutron Fourier maps clearly showed the details of an extensive set of H bonds involving the ND3+ terminus that may contribute to the unusual thermostability of this molecule. |
==About this Structure== | ==About this Structure== | ||
| - | 1VCX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus] with FE and DOD as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1VCX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus] with <scene name='pdbligand=FE:'>FE</scene> and <scene name='pdbligand=DOD:'>DOD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCX OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Pyrococcus furiosus]] | [[Category: Pyrococcus furiosus]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Adams, M | + | [[Category: Adams, M W.W.]] |
[[Category: Bau, R.]] | [[Category: Bau, R.]] | ||
[[Category: Chatake, T.]] | [[Category: Chatake, T.]] | ||
| - | [[Category: Jr., F | + | [[Category: Jr., F E.Jenney.]] |
[[Category: Kurihara, K.]] | [[Category: Kurihara, K.]] | ||
[[Category: Moiseeva, N.]] | [[Category: Moiseeva, N.]] | ||
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[[Category: neutron structure]] | [[Category: neutron structure]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:33:55 2008'' |
Revision as of 13:33, 21 February 2008
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Neutron Crystal Structure of the Wild Type Rubredoxin from Pyrococcus Furiosus at 1.5A Resolution
Overview
The structure of a partially deuterated rubredoxin from the hyperthermophilic archaeon Pyrococcus furiosus, an organism that grows optimally at 100 degrees C, was determined by using the neutron single-crystal diffractometer dedicated for biological macromolecules (BIX-3) at the JRR-3M reactor of the Japan Atomic Energy Research Institute. Data were collected at room temperature up to a resolution of 1.5 A, and the completeness factor of the data set was 81.9%. The model contains 306 H and 50 D atoms. A total of 37 hydration water molecules were identified, with 15 having all three atoms fully located and the remaining D2O molecules partially defined. The model has been refined to final agreement factors of R = 18.6% and Rfree = 21.7%. Several orientations of the O-D bonds of side chains, whose assignments from x-ray data were previously ambiguous, were clearly visible in the neutron structure. Although most backbone N-H bonds had undergone some degree of H/D exchange throughout the rubredoxin molecule, 5 H atom positions still had distinctly negative (H) peaks. The neutron Fourier maps clearly showed the details of an extensive set of H bonds involving the ND3+ terminus that may contribute to the unusual thermostability of this molecule.
About this Structure
1VCX is a Single protein structure of sequence from Pyrococcus furiosus with and as ligands. Full crystallographic information is available from OCA.
Reference
Neutron crystallographic study on rubredoxin from Pyrococcus furiosus by BIX-3, a single-crystal diffractometer for biomacromolecules., Kurihara K, Tanaka I, Chatake T, Adams MW, Jenney FE Jr, Moiseeva N, Bau R, Niimura N, Proc Natl Acad Sci U S A. 2004 Aug 3;101(31):11215-20. Epub 2004 Jul 22. PMID:15272083
Page seeded by OCA on Thu Feb 21 15:33:55 2008
Categories: Pyrococcus furiosus | Single protein | Adams, M W.W. | Bau, R. | Chatake, T. | Jr., F E.Jenney. | Kurihara, K. | Moiseeva, N. | Niimura, N. | Tanaka, I. | DOD | FE | Hydration water structure | Hydrogen atom position | Hydrogen/deuterium exchange | Iron-sulfur core | N-terminal region | Neutron structure
