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Neutron crystallographic study on rubredoxin from ${it Pyrococcus furiosus}$ by BIX-3, a single-crystal diffractometer for biomacromolecules

Kurihara, Kazuo; Tanaka, Ichiro*; Chatake, Toshiyuki*; Adams, M. W. W.*; Jenney, F. E. Jr.*; Moiseeva, N.*; Bau, R.*; Niimura, Nobuo

The structure of a rubredoxin (Rd) from ${it Pyrococcus furiosus}$, an organism that grows optimally at 100 $$^{circ}$$C, was determined using the neutron single-crystal diffractometer for biological macromolecules (BIX-3) at the JRR-3 reactor of JAERI. Data were collected at room temperature up to a resolution of 1.5 ${AA}$, and the completeness of the data set was 81.9 %. The model contains 306 H atoms and 50 D atoms. A total of 37 hydration water molecules were identified. The model has been refined to final agreement factors of ${it R}$ = 18.6 % and ${it R}$$$_{free}$$ = 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. While most backbone N-H bonds had undergone some degree of H/D exchange throughout the molecule, five 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 ND$$_{3}$$$$^{+}$$ terminus that may contribute to the unusual thermostability of this molecule.

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