Pasteurella multocida toxin (PMT) is one of virulence factors responsible for the pathogenesis in some Pasteurellosis. We determined the crystal structure of the C-terminal region of PMT (C-PMT), which carries an intracellularly active moiety. The overall structure of C-PMT displays three different domains designated C1, C2 and C3. We found in the C3 domain the Cys-His-Asp catalytic triad that is organized only when the Cys is released from a disulfide bond. The steric alignment of the triad corresponded well to that of papain or other enzymes carrying the Cys-His-Asp triad. Our results demonstrate that PMT is an enzymatic toxin carrying the cysteine-protease like catalytic triad, which is organized only under reducing conditions.
Weathering steel, when exposed outdoors for a few years, forms a protective layer resulting in reduction of the corrosion rate. The state of rusts is fundamental for understanding its mechanism, but the structure and its relationship with the mechanism have not been understood. In this study, a new crystallographic approach was applied to reveal nano-structure of rusts with using of X-ray synchrotron radiation. It has been shown that additional elements alter the corrosion process in its early stage, resulting in formation of protective rusts.
The crystal structures have been determined systematically for mononuclear copper (II) complexes incorporated various ethylenediamine ligands and several cyanide-bridged bimetallic assemblies with linear one-dimensional, zigzag one-dimensional, two-dimensional, and co-crystals of mononuclear and one-dimensional complexes. The temperature dependence of molecular crystal lattices and local pseudo Jahn-Teller distortion were elucidated that larger tetragonally distorted chromophores, associated with ground electronic states, exhibited smaller structural changes by cooling temperature for the present systems in a solid-state matrix. On the other hand, characters of coordination bonds as well as structural distortion for copper ions in metalloproteins in a flexible polypeptide matrix usually. By comparing with them, we discuss the role of matrix for tuning geometric and electronic structures of functional copper (II) ions showing Jahn-Teller distortion.
Structural information of biological macromolecules at an atomic level is indispensable for the current biological studies. In order to investigate the practicality of ultra-high energy X-rays (-35 keV) in protein crystallography, Xe-MAD and I-MAD experiments were performed at the synchrotron facility, SPring-8. The electron density maps for both cases were sufficient enough for auto-tracing of protein structures. Therefore, the use of ultra-high energy X-rays can provide significant development to the high-throughput structure determination of macromolecules. Other studies using ultra-high energy X-rays in protein crystallography are also reviewed in this report.
The single crystal of the pseudorotaxane derivative, which consists of a crown ether and N- (xylyl) aminomethylferrocene derivative shows reversible single crystal-to-single crystal first order phase transition. The transformation brings about change of the optical properties of the crystal; transmittance of polarized light shed on the (001) face is increased and decreased by the change of temperature around the Tc (128°C) . At the high temperature phase, the optical anisotropic parameter of birefringence of the crystal is smaller than that at low temperature phase. The connection of the phase transition and the optical property shows potential use of the material as a thermo-optic switch. The thermo-optic switching performance of the crystals is able to be repeated for at least 10 times. Using the newly developed very rapid single crystal diffraction technique, the structures before and after the phase transition have been analyzed. The p-tolyl and phenylene groups are aligned almost perpendicular to the (001) face at the low temperature phase. At the high temperature phase, on the other hand, all the p-tolyl groups of the axle molecules in the crystal rotate at the same direction against the (001) face. The optical switching results from this collective harmonic rotation of the p-tolyl groups.
Structural refinement of macromolecules is difficult because the observation-to-parameter ratio is usually low (typically about 3-5) . In most cases, manual intervention is required in the multiple rounds as a complementary function to the refinement algorithms. This manual intervention including linking and/or extending the fragments of the initial model and fitting ill-matched residues using computer graphics, is both consuming time and requiring a great deal of expertise in crystallography. For realizing the manual-intervention-free refinement, we have developed a new automatic refinement software package, LAFIRE (Local-correlation-coefficient-based Automatic Fltting for REfinement program) . This software was designed to perform the whole process of protein structural refinement automatically with the refinement programs CNS or REFMAC5 from an initial model that can be approximate, fragmentary or even only main chain. By using LAFIRE, a full-or semi-automatic refinement process can be realized within a few hours or days. The overall strategies and methods used in LAFIRE are presented, and the future development of LAFIRE is also discussed here.
Neutron powder diffraction, quasi elastic and inelastic scattering measurements were performed to examine the mechanism of phase transition and protonic conduction of K3H (SeO4) 2. SeO4 tetrahedra in the high-temperature phase (phase I) were rotationally displaced with the occupancy 1/3 and the crystal structure in the room temperature phase (phase II) remained locally. Proton distribution maps obtained from MEM describe that 13.4% of protons exist at inter-layer space. Proton diffusion constants were estimated as 1.9 (1) × 10-10 m2/s at 393 K and 2.1 (3) × 10-10 m2/s at 413 K respectively. A rotational mode of SeO4 tetrahedra causes change from R3m to C2/c. No soft mode was observed both of transversal acoustic and zone boundary optical modes, however, a diffusive spectrum was observed around 0 meV at the L-point (0.5 2 0) above Tc as an over-dumped phonon mode. The rotational mode of SeO4 tetrahedra drives the improper ferroelastic phase transition, and assists the disconnection and reconstruction of hydrogen bonds in the phase I.