Journal of Synchrotron Radiation

Volume 20, Part 6 (November 2013)


4th International Symposium on Diffraction Structural Biology (ISDSB2013)

Fukiage Hall, Nagoya, Japan, 26-29 May 2013

[Buy print version] A printed copy of this issue is available for purchase


[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Images from presentations given at ISDSB2013. Centre: structure of the [beta]-2 adrenergic receptor in complex with its G protein (courtesy of B. Kobilka); ESRF played a major role in the initial GPCR crystal structure determined by the Brian Kobilka Lab, with subsequent structures being obtained with data collected at APS. Top left: an X-ray free-electron laser simulated diffraction pattern with quantum noise for the 70S ribosome (see Tokuhisa et al., pages 899-904). Top right: 2|Fo| - |Fc| neutron-scattering-length map around the active site of RNase A (see Kusaka et al., pages 994-998). Bottom left: slice through the reconstructed tomographic volume of a cryo-EM/ET observation of an RDV-infected NC24 cell (see Miyazaki et al., pages 826-828). Bottom right: time-of-flight neutron diffraction image of transthyretin recorded by iBIX (Yokoyama et al., pages 834-837).

diffraction structural biology


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J. Synchrotron Rad. (2013). 20, 819  [ doi:10.1107/S0909049513025478 ]

Diffraction structural biology - a new horizon

T. Yamane, J. R. Helliwell, J. E. Johnson, N. Yasuoka and N. Sakabe

Synopsis: An introductory overview to the special issue papers on diffraction structural biology in this issue of the journal.

Online 11 October 2013


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J. Synchrotron Rad. (2013). 20, 820-825  [ doi:10.1107/S0909049513021833 ]

Sub-millisecond time-resolved SAXS using a continuous-flow mixer and X-ray microbeam

R. Graceffa, R. P. Nobrega, R. A. Barrea, S. V. Kathuria, S. Chakravarthy, O. Bilsel and T. C. Irving

Synopsis: The development of a high-duty-cycle microsecond time-resolution SAXS capability at the Biophysics Collaborative Access Team beamline (BioCAT) 18ID at the Advanced Photon Source, Argonne National Laboratory, USA, is reported.

Online 1 October 2013


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J. Synchrotron Rad. (2013). 20, 826-828  [ doi:10.1107/S090904951302219X ]

Cryo-electron tomography: moving towards revealing the viral life cycle of Rice dwarf virus

N. Miyazaki, F. Akita, A. Nakagawa, K. Murata, T. Omura and K. Iwasaki

Synopsis: The viral and virus-related structures of Rice dwarf virus have been visualized by cryo-electron microscopy and tomography revealing the viral infection and replication mechanisms.

Online 2 October 2013


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[HTML version][PDF version][Supplementary Material]  [Open access]

J. Synchrotron Rad. (2013). 20, 829-833  [ doi:10.1107/S0909049513022188 ]

U-shape rotating anti-cathode compact X-ray generator: 20 times stronger than the commercially available X-ray source

N. Sakabe, K. Sakabe, S. Ohsawa, T. Sakai, H. Kobayakawa, T. Sugimura, M. Ikeda, M. Tawada, N. Watanabe, K. Sasaki and M. Wakatsuki

Synopsis: A new type of U-shape anti-cathode X-ray generator in which the inner surface of a cylindrical target is irradiated by an electron beam has been made by modifying a conventional rotating anti-cathode X-ray generator whose brightness in the catalog is 12 kW mm-2. A brightness of 129 kW mm-2 was thereby obtained with this new U-shape-type X-ray generator. This new X-ray generator is expected to be of keen interest for applications in academia, industry and in hospitals.

Online 2 October 2013


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J. Synchrotron Rad. (2013). 20, 834-837  [ doi:10.1107/S090904951302075X ]

Hydrogen-bond network and pH sensitivity in human transthyretin

T. Yokoyama, M. Mizuguchi, Y. Nabeshima, K. Kusaka, T. Yamada, T. Hosoya, T. Ohhara, K. Kurihara, I. Tanaka and N. Niimura

Synopsis: The neutron crystal structure of human transthyretin is presented.

Online 29 September 2013


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J. Synchrotron Rad. (2013). 20, 838-842  [ doi:10.1107/S0909049513020797 ]

New methodologies at PF AR-NW12A: the implementation of high-pressure macromolecular crystallography

L. M. G. Chavas, T. Nagae, H. Yamada, N. Watanabe, Y. Yamada, M. Hiraki and N. Matsugaki

Synopsis: The evolution of AR-NW12A into a multi-purpose end-station with optional high-pressure crystallography is described.

Online 1 October 2013


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J. Synchrotron Rad. (2013). 20, 843-847  [ doi:10.1107/S0909049513021572 ]

Structural studies of haemoglobin from pisces species shortfin mako shark (Isurus oxyrinchus) at 1.9 Å resolution

P. Ramesh, S. S. Sundaresan, P. Sathya Moorthy, M. Balasubramanian and M. N. Ponnuswamy

Synopsis: Shortfin mako shark haemoglobin adopts an unliganded deoxy T state conformation, which is shown from the quaternary structural features, interface interactions and heme binding sites of different subunits of haemoglobin with high-resolution X-ray data.

PDB reference: 3mkb

Online 1 October 2013


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J. Synchrotron Rad. (2013). 20, 848-853  [ doi:10.1107/S0909049513020761 ]

Morphological image processing for quantitative shape analysis of biomedical structures: effective contrast enhancement

Y. Kimori

Synopsis: A contrast enhancement approach utilizing a new type of mathematical morphology called rotational morphological processing is introduced. The method is quantitatively evaluated and then applied to some medical images.

Online 25 September 2013


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J. Synchrotron Rad. (2013). 20, 854-858  [ doi:10.1107/S0909049513020694 ]

Crystal structure analysis, overexpression and refolding behaviour of a DING protein with single mutation

Z. Gai, A. Nakamura, Y. Tanaka, N. Hirano, I. Tanaka and M. Yao

Synopsis: Crystals of a member of the DING protein family (HPBP) were obtained accidentally, and the structure was determined at 1.35 Å resolution. For further analysis, a system for preparation of HPBP was constructed and the structure of a prepared sample was confirmed by X-ray crystal structure analysis at 1.03 Å resolution.

PDB references: 3w9w and 3w9v

Online 29 September 2013


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J. Synchrotron Rad. (2013). 20, 859-863  [ doi:10.1107/S0909049513020943 ]

Phase-diagram-guided method for growth of a large crystal of glycoside hydrolase family 45 inverting cellulase suitable for neutron structural analysis

A. Nakamura, T. Ishida, S. Fushinobu, K. Kusaka, I. Tanaka, K. Inaka, Y. Higuchi, M. Masaki, K. Ohta, S. Kaneko, N. Niimura, K. Igarashi and M. Samajima

Synopsis: The crystallization-phase-diagram-guided method is effective for growing large protein crystals for neutron protein crystallography.

Online 25 September 2013


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J. Synchrotron Rad. (2013). 20, 864-868  [ doi:10.1107/S0909049513020773 ]

Structural fluctuation observed in Z-DNA d(CGCGCG)2 in the absence of divalent metal cations and polyamines

T. Chatake

Synopsis: Various structural fluctuations of phosphate groups and hydration in the minor groove were observed in the crystal structure of Z-DNA in the absence of divalent metal cations and polyamines.

PDB reference: 3wbo

Online 25 September 2013


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J. Synchrotron Rad. (2013). 20, 869-874  [ doi:10.1107/S0909049513020827 ]

Structure of liposome encapsulating proteins characterized by X-ray scattering and shell-modeling

M. Hirai, R. Kimura, K. Takeuchi, Y. Hagiwara, R. Kawai-Hirai, N. Ohta, N. Igarashi and N. Shimuzu

Synopsis: Wide-angle X-ray scattering data using a third-generation synchrotron radiation source are presented.

Online 26 September 2013


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J. Synchrotron Rad. (2013). 20, 875-879  [ doi:10.1107/S0909049513020700 ]

X-ray structure determination and deuteration of nattokinase

Y. Yanagisawa, T. Chatake, S. Naito, T. Ohsugi, C. Yatagai, H. Sumi, A. Kawaguchi, K. Chiba-Kamosida, M. Ogawa, T. Adachi and Y. Morimoto

Synopsis: X-ray structure determination and deuteration of nattokinase were performed to facilitate neutron crystallographic analysis.

PDB reference: 4dww

Online 25 September 2013


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J. Synchrotron Rad. (2013). 20, 880-883  [ doi:10.1107/S0909049513020724 ]

Experiences with archived raw diffraction images data: capturing cisplatin after chemical conversion of carboplatin in high salt conditions for a protein crystal

S. W. M. Tanley, K. Diederichs, L. M. J. Kroon-Batenburg, A. M. M. Schreurs and J. R. Helliwell

Synopsis: Archiving of raw diffraction images data has led to new structural chemistry information being obtained for previously published results, which leads to the conclusion that carboplatin has partially converted to cisplatin in the high NaCl concentration conditions used in the crystallization procedure.

Online 1 October 2013


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J. Synchrotron Rad. (2013). 20, 884-889  [ doi:10.1107/S0909049513021110 ]

Crystal structure of endo-1,4-[beta]-glucanase from Eisenia fetida

T. Arimori, A. Ito, M. Nakazawa, M. Ueda and T. Tamada

Synopsis: The crystal structure of endo-1,4-[beta]-glucanase from the earthworm Eisenia fetida, which retained sufficient cellulase activity at low temperature, was determined at 1.5 Å resolution.

PDB reference: 3wc3

Online 1 October 2013


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J. Synchrotron Rad. (2013). 20, 890-893  [ doi:10.1107/S0909049513021067 ]

Improvement of an automated protein crystal exchange system PAM for high-throughput data collection

M. Hiraki, Y. Yamada, L. M. G. Chavas, S. Wakatsuki and N. Matsugaki

Synopsis: A special liquid-nitrogen Dewar with double capacity for the sample-exchange robot has been created at AR-NE3A at the Photon Factory, allowing continuous fully automated data collection. In this work, this new system is described and the stability of its calibration is discussed.

Online 1 October 2013


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J. Synchrotron Rad. (2013). 20, 894-898  [ doi:10.1107/S0909049513020712 ]

Crystal structure of UDP-glucose:anthocyanidin 3-O-glucosyltransferase from Clitoria ternatea

T. Hiromoto, E. Honjo, T. Tamada, N. Noda, K. Kazuma, M. Suzuki and R. Kuroki

Synopsis: The anthocyanidin 3-O-glucosyltransferase from Clitoria ternatea (Ct3GT-A) was expressed in Escherichia coli, and the three-dimensional structure of Ct3GT-A was determined using X-ray crystallography. This report describes the architecture of Ct3GT-A, including the structures of the donor- and acceptor-binding sites.

PDB reference: 3wc4

Online 29 September 2013


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J. Synchrotron Rad. (2013). 20, 899-904  [ doi:10.1107/S0909049513022152 ]

High-speed classification of coherent X-ray diffraction patterns on the K computer for high-resolution single biomolecule imaging

A. Tokuhisa, J. Arai, Y. Joti, Y. Ohno, T. Kameyama, K. Yamamoto, M. Hatanaka, B. Gerofi, A. Shimada, M. Kurokawa, F. Shoji, K. Okada, T. Sugimoto, M. Yamaga, R. Tanaka, M. Yokokawa, A. Hori, Y. Ishikawa, T. Hatsui and N. Go

Synopsis: A code with an algorithm for high-speed classification of X-ray diffraction patterns has been developed. Results obtained for a set of 1 × 106 simulated diffraction patterns are also reported.

Online 3 October 2013


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J. Synchrotron Rad. (2013). 20, 905-909  [ doi:10.1107/S0909049513020736 ]

Crystal structure of human cyclin-dependent kinase-2 complex with MK2 inhibitor TEI-I01800: insight into the selectivity

A. Fujino, K. Fukushima, T. Kubota, T. Kosugi and M. Takimoto-Kamimura

Synopsis: The Gly-rich loop of cyclin-dependent kinase 2 (CDK2) bound to TEI-I01800 as an MK2 specific inhibitor forms a [beta]-sheet which is a common structure in CDK2-ligand complexes. Here, the reason why TEI-I01800 does not become a strong inhibitor against CDK2 based on the conformation of TEI-I01800 is presented.

PDB reference: 3wbl

Online 26 September 2013


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J. Synchrotron Rad. (2013). 20, 910-913  [ doi:10.1107/S0909049513022176 ]

SPring-8 BL41XU, a high-flux macromolecular crystallography beamline

K. Hasegawa, N. Shimizu, H. Okumura, N. Mizuno, S. Baba, K. Hirata, T. Takeuchi, H. Yamazaki, Y. Senba, H. Ohashi, M. Yamamoto and T. Kumasaka

Synopsis: SPring-8 BL41XU provides a high-flux X-ray beam of size 10-50 µm, and enables high-quality diffraction data to be obtained from various types of protein crystals. Details of this beamline and an upgrade project are described.

Online 2 October 2013


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J. Synchrotron Rad. (2013). 20, 914-918  [ doi:10.1107/S0909049513020748 ]

Crystal structure of a complex of human chymase with its benzimidazole derived inhibitor

Y. Matsumoto, S. Kakuda, M. Koizumi, T. Mizuno, Y. Muroga, T. Kawamura and M. Takimoto-Kamimura

Synopsis: The crystal structure of human chymase complexed with a novel benzimidazole inhibitor, TJK002, was determined at 2.8 Å resolution. The present study shows that the benzimidazole ring of the inhibitor takes the stable stacking interaction with the protonated His57 in the catalytic domain of human chymase.

PDB reference: 4kp0

Online 25 September 2013


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J. Synchrotron Rad. (2013). 20, 919-922  [ doi:10.1107/S0909049513022772 ]

Modulation of the intermolecular interaction of myoglobin by removal of the heme

H. Imamura, T. Morita, T. Sumi, Y. Isogai, M. Kato and K. Nishikawa

Synopsis: The present study analysed small-angle X-ray scattering profiles of myoglobin to examine how removal of the heme changes the intermolecular interaction.

Online 2 October 2013


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J. Synchrotron Rad. (2013). 20, 923-928  [ doi:10.1107/S0909049513021298 ]

Structure of the human-heart fatty-acid-binding protein 3 in complex with the fluorescent probe 1-anilinonaphthalene-8-sulphonic acid

M. Hirose, S. Sugiyama, H. Ishida, M. Niiyama, D. Matsuoka, T. Hara, E. Mizohata, S. Murakami, T. Inoue, S. Matsuoka and M. Murata

Synopsis: The crystal structure of human-heart-type fatty-acid-binding protein in complex with anilinonaphthalene-8-sulfonate was solved at 2.15 Å resolution revealing the detailed binding mechanism of the fluorescent probe 1-anilinonaphthalene-8-sulfonate.

PDB reference: 3wbg

Online 1 October 2013


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J. Synchrotron Rad. (2013). 20, 929-932  [ doi:10.1107/S0909049513021341 ]

A docking study of enhanced intracellular survival protein from Mycobacterium tuberculosis with human DUSP16/MKP-7

H.-J. Yoon, K. H. Kim, J. K. Yang, S. W. Suh, H. Kim and S. Jang

Synopsis: A docking study of Mtb Eis with its substrate DUSP16/MKP-7 was performed. The docking model suggests dissociation of hexameric Mtb Eis into dimers or monomers.

Online 1 October 2013


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J. Synchrotron Rad. (2013). 20, 933-937  [ doi:10.1107/S0909049513021328 ]

Structural and biochemical analysis of a thermostable membrane-bound stomatin-specific protease

H. Yokoyama, D. Kobayashi, N. Takizawa, S. Fujii and I. Matsui

Synopsis: According to the structural and biochemical analysis of the stomatin-specific protease 1510-N, two degraded products were produced via acyl-enzyme intermediates. The N-terminal half of the substrate peptide binds to 1510-N more tightly than the C-terminal half of the peptide.

PDB reference: 3wg5

Online 25 September 2013


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J. Synchrotron Rad. (2013). 20, 938-942  [ doi:10.1107/S0909049513022875 ]

Improvements toward highly accurate diffraction experiments at the macromolecular micro-crystallography beamline BL-17A

Y. Yamada, L. M. G. Chavas, N. Igarashi, M. Hiraki, S. Wakatsuki and N. Matsugaki

Synopsis: The BL-17A macromolecular crystallography beamline at the Photon Factory was updated to improve the accuracy of diffraction experiments conducted using tiny crystals.

Online 8 October 2013


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J. Synchrotron Rad. (2013). 20, 943-947  [ doi:10.1107/S090904951302133X ]

Structure basis 1/2SLPI and porcine pancreas trypsin interaction

K. Fukushima, T. Kamimura and M. Takimoto-Kamimura

Synopsis: 1/2SLPI is a C-terminal domain of SLPI (secretory leukocyte protease inhibitor) which inhibits various serine proteases broadly. The present study is the first X-ray structural report on how 1/2SLPI with P1 Leu strongly inhibits trypsin and how it can inhibit multiple serine proteases.

PDB reference: 4doq

Online 29 September 2013


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J. Synchrotron Rad. (2013). 20, 948-952  [ doi:10.1107/S0909049513022887 ]

Development of an online UV-visible microspectrophotometer for a macromolecular crystallography beamline

N. Shimizu, T. Shimizu, S. Baba, K. Hasegawa, M. Yamamoto and T. Kumasaka

Synopsis: An online UV-visible microspectrophotometer has been developed for the macromolecular crystallography beamline at SPring-8. Details of this spectrophotometer are reported.

Online 2 October 2013


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J. Synchrotron Rad. (2013). 20, 953-957  [ doi:10.1107/S0909049513022164 ]

Creation and structure determination of an artificial protein with three complete sequence repeats

M. Adachi, R. Shimizu, R. Kuroki and M. Blaber

Synopsis: An artificial protein with three complete sequence repeats was created and the structure was determined by X-ray crystallography. The structure showed threefold symmetry even though there is an amino- and carboxy-terminal. The artificial protein with threefold symmetry may be useful as a scaffold to capture small materials with C3 symmetry.

Online 8 October 2013


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J. Synchrotron Rad. (2013). 20, 958-961  [ doi:10.1107/S0909049513020815 ]

Fundamental studies for the proton polarization technique in neutron protein crystallography

I. Tanaka, K. Kusaka, T. Chatake and N. Niimura

Synopsis: Fundamental trials to realise the proton polarization technique for detecting hydrogen with higher sensitivity in neutron protein crystallography are described.

Online 2 October 2013


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J. Synchrotron Rad. (2013). 20, 962-967  [ doi:10.1107/S0909049513020803 ]

High-resolution crystal structure of Streptococcus pyogenes [beta]-NAD+ glycohydrolase in complex with its endogenous inhibitor IFS reveals a highly water-rich interface

J. Y. Yoon, D. R. An, H.-J. Yoon, H. S. Kim, S. J. Lee, H. N. Im, J. Y. Jang and S. W. Suh

Synopsis: The crystal structure of the complex between the C-terminal domain of Streptococcus pyogenes [beta]-NAD+ glycohydrolase and an endogenous inhibitor for SPN was determined at 1.70 Å. It reveals that the interface between the two proteins is highly rich in water molecules.

PDB reference: 4kt6

Online 29 September 2013


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J. Synchrotron Rad. (2013). 20, 968-973  [ doi:10.1107/S0909049513021596 ]

JAXA protein crystallization in space: ongoing improvements for growing high-quality crystals

S. Takahashi, K. Ohta, N. Furubayashi, B. Yan, M. Koga, Y. Wada, M. Yamada, K. Inaka, H. Tanaka, H. Miyoshi, T. Kobayashi and S. Kamigaichi

Synopsis: The Japan Aerospace Exploration Agency's `high-quality protein crystal growth' project is introduced. If crystallization conditions were carefully fixed in ground-based experiments, high-quality protein crystals grew in microgravity in many experiments on the International Space Station, especially when a highly homogeneous protein sample and a viscous crystallization solution were employed.

Online 26 September 2013


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J. Synchrotron Rad. (2013). 20, 974-979  [ doi:10.1107/S0909049513020785 ]

Crystal structure of human CK2[alpha] at 1.06 Å resolution

T. Kinoshita, T. Nakaniwa, Y. Sekiguchi, Y. Sogabe, A. Sakurai, S. Nakamura and I. Nakanishi

Synopsis: The high-resolution crystal structure of the human CK2 catalytic subunit reveals the structural insights that probably promote drug discovery.

PDB reference: 3war

Online 2 October 2013


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J. Synchrotron Rad. (2013). 20, 980-983  [ doi:10.1107/S0909049513023741 ]

Real-time investigation of protein unfolding at an air-water interface at the 1 s time scale

Y. F. Yano, E. Arakawa, W. Voegeli and T. Matsushita

Synopsis: Protein unfolding at an air-water interface is followed in real time by a recently developed simultaneous multiple-angle-wavelength-dispersive X-ray reflectometer with a time resolution of 1 s.

Online 2 October 2013


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J. Synchrotron Rad. (2013). 20, 984-988  [ doi:10.1107/S0909049513022760 ]

Crystal structure of the N-terminal domain of MinC dimerized via domain swapping

J. Y. An, T. G. Kim, K. R. Park, J.-G. Lee, H.-S. Youn, Y. Lee, J. Y. Kang, G. B. Kang and S. H. Eom

Synopsis: The crystal structure of EcoMinCNTD dimerized via domain swapping was solved at 2.3 Å resolution. The present study suggests that EcoMinC dimerizes through both EcoMinCNTD and EcoMinCCTD.

PDB reference: 4l1c

Online 2 October 2013


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J. Synchrotron Rad. (2013). 20, 989-993  [ doi:10.1107/S090904951302373X ]

High-resolution X-ray crystal structure of bovine H-protein using the high-pressure cryocooling method

A. Higashiura, K. Ohta, M. Masaki, M. Sato, K. Inaka, H. Tanaka and A. Nakagawa

Synopsis: Using the high-pressure cryocooling method, the high-resolution X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. This is the first ultra-high-resolution structure obtained from a high-pressure cryocooled crystal.

PDB reference: 3wdn

Online 5 October 2013


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J. Synchrotron Rad. (2013). 20, 994-998  [ doi:10.1107/S0909049513021845 ]

Evaluation of performance for IBARAKI biological crystal diffractometer iBIX with new detectors

K. Kusaka, T. Hosoya, T. Yamada, K. Tomoyori, T. Ohhara, M. Katagiri, K. Kurihara, I. Tanaka and N. Niimura

Synopsis: The time-of-flight neutron single-crystal diffractometer iBIX at the next-generation neutron source J-PARC has been upgraded and is available for user experiments on protein samples in particular. Neutron structure analysis of a standard protein sample was carried out in order to evaluate the performance of iBIX.

Online 11 October 2013


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J. Synchrotron Rad. (2013). 20, 999-1002  [ doi:10.1107/S0909049513021584 ]

A convenient tool for gas derivatization using fine-needle capillary mounting for protein crystals

N. Mizuno, M. Makino and T. Kumasaka

Synopsis: A convenient gas-derivatization tool for protein crystals is presented in combination with a fine-needle capillary and a gas-pressure regulator.

Online 1 October 2013


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J. Synchrotron Rad. (2013). 20, 1003-1009  [ doi:10.1107/S0909049513022784 ]

Numerical model of protein crystal growth in a diffusive field such as the microgravity environment

H. Tanaka, S. Sasaki, S. Takahashi, K. Inaka, Y. Wada, M. Yamada, K. Ohta, H. Miyoshi, T. Kobayashi and S. Kamigaichi

Synopsis: Numerical analysis of the concentration depletion zones in a transient state suggested that, in microgravity, protein crystals grow in a lower supersaturation and the impurity ratio decreases in the centre of the crystal.

Online 1 October 2013


current events


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J. Synchrotron Rad. (2013). 20, 1010-1011  [ doi:10.1107/S0909049513027623 ]

Current events

Online 10 October 2013


 

J. Synchrotron Rad. (2013). 20, 1012

forthcoming meetings and short courses


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