Nihon Kessho Gakkaishi
Online ISSN : 1884-5576
Print ISSN : 0369-4585
ISSN-L : 0369-4585
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Showing 1-15 articles out of 15 articles from the selected issue
Preface
Current Topics in Crystallography
Review Articles
Review Articles
  • Satoshi WATANABE, Kunio MIKI
    2020 Volume 62 Issue 2 Pages 91-98
    Published: May 31, 2020
    Released: May 31, 2020
    JOURNALS FREE ACCESS

    Approximately one-half of all proteins in cells require specific metal ions for proper function, which are delivered by specific auxiliary proteins called metallochaperones. Hydrogen producing enzymes, [NiFe] hydrogenases harbor a complex metal cofactor, NiFe(CN)2CO, in their active sites. Assembly and incorporation of the NiFe(CN)2CO center requires specific maturation machinery, in which six Hyp proteins (HypABCDEF) play key roles. Four Hyp proteins (HypC-HypF) are involved in the biosynthesis and incorporation of the Fe(CN)2CO group. After Fe insertion, HypA and HypB insert the Ni ion into the hydrogenase large subunit. Here, we review recent structural studies of Hyp protein complexes for [NiFe] hydrogenase maturation.

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Accurate Crystal Structure Analysis
  • Nobuo KAMIYA
    2020 Volume 62 Issue 2 Pages 99-105
    Published: May 31, 2020
    Released: May 31, 2020
    JOURNALS FREE ACCESS
    Supplementary material

    ADP-Ribose pyrophosphatase reaction was traced by cryo-trapping protein crystallography at atomic resolutions around 1 Å. Several intermediate states were identified but dynamic structure changes in a climax of the hydration reaction were blurred by instabilities of the transition state. Crystal structures of photosystem II (PSII) were resolved at resolutions around 1.9 Å. Two structures of the oxygen-evolving complex (OEC) in a PSII homodimer were clearly different in an asymmetric unit under a threshold of radiation dose, 0.12 MGy, although the polypeptide frameworks of PSII, surrounding the OEC, were the same with each other. The reaction mechanism of ADPRase and the OEC structure alteration of PSII were discussed considering atomic parameter errors and reliabilities of their structures.

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  • Kiyofumi TAKABA, Kazuya HASEGAWA, Kazuki TAKEDA
    2020 Volume 62 Issue 2 Pages 106-111
    Published: May 31, 2020
    Released: May 31, 2020
    JOURNALS FREE ACCESS
    Supplementary material

    The electron density distribution of each atom reflects chemical properties of the atom in the molecule. The charge-density analysis at ultra-high resolution can analyze details of the electronic distribution even in protein molecules. In this paper, we introduce a recent our result for the charge density analysis of green fluorescent protein (GFP) at an ultra-high resolution of 0.78 Å. The precise electron density distribution gives information about CH-π and lone pair-π interactions and CH…O/N type non-conventional hydrogen bonds as well as conventional hydrogen bonds. The information about such weak but substantial interactions between the chromophore and the protein environment explains the properties of GFP.

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  • Seiya SHIMONO, Hiroki ISHIBASHI, Yoshiki KUBOTA, Shogo KAWAGUCHI
    2020 Volume 62 Issue 2 Pages 112-117
    Published: May 31, 2020
    Released: May 31, 2020
    JOURNALS FREE ACCESS

    High-resolution powder diffractometry is a powerful method to determine the accurate crystal system and crystal structures. Neutron powder diffraction using TOF neutron diffractometer (SuperHRPD) in MLF at J-PARC and X-ray powder diffraction using Debye-Scherrer diffractometer with one-dimensional MYTHEN detector at SPring-8 are introduced. We successfully observed the structural phase transitions accompanied by small crystal distortion in spinel oxide CoV2O4 and its substitution system by combination of these measurements and clarify the nature of the phase transition of CoV2O4.

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