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Journal Articles

A Neutron crystallographic analysis of a rubredoxin mutant at 1.6 resolution

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

Acta Crystallographica Section D, 60(8), p.1364 - 1373, 2004/08

https://doi.org/10.1107/S090744490401176X

Times Cited Count：34 Percentile：88.89(Biochemical Research Methods)

A neutron diffraction study has been carried out at 1.6 resolution on a mutant rubredoxin from using the BIX-3 single-crystal diffractometer at the JRR-3 reactor of JAERI. In order to study the unusual thermostability of rubredoxin from , the hydrogen-bonding patterns were compared between the native and a 'triple-mutant' variant where three residues were changed so that they are identical to those in a mesophilic rubredoxin. In the present study, some minor changes were found between the wild-type and mutant proteins in the hydrogen-bonding patterns of the Trp3/Tyr3 region. The H/D-exchange ratios in the protein were also studied. The results suggest that the backbone amide bonds near the four Cys residues of the FeS $_{4}$ redox center are most resistant to H/D exchange. In addition, the 1.6 resolution of the present neutron structure determination has revealed a more detailed picture than previously available of some portions of the water structure, including ordered and disordered O-D bonds.

Journal Articles

Neutron crystallographic study on rubredoxin from 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

Proceedings of the National Academy of Sciences of the United States of America, 101(31), p.11215 - 11220, 2004/08

https://doi.org/10.1073/pnas.0403807101

Times Cited Count：48 Percentile：61.13(Multidisciplinary Sciences)

The structure of a rubredoxin (Rd) from , 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 , 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 = 18.6 % and $_{free}$ = 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.

Journal Articles

Neutron diffraction study on the structure of rubredoxin from it Pyrococcus furiosus

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

Journal of the Physical Society of Japan, Vol.70, Supplement A, p.400 - 402, 2001/05

With the new single-crystal diffractometer BIX-3 at the JRR-3M reactor of JAERI, a single-crystal neutron diffraction analysis of the structure of the small protein rubredoxin from the hyperthermophile Pyrococcus furiosus is currently under way. Data were collected at room temperature up to a resolution of 1.5 intervals in and exposure times ranging from 60 to 77 minutes per frame. The completeness factor of the 1.5-. Included in the refinement are 301 hydrogen atoms and 40 deuterium atoms, and 29 water molecules were also identified. In the present model, the current value for R and R are 24.0 and 26.3 , respectively.