issue contents

Journal logoJOURNAL OF
ISSN: 1600-5775

November 2013 issue

4th International Symposium on Diffraction Structural Biology (ISDSB2013)

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

Highlighted 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).

facility information

diffraction structural biology

J. Synchrotron Rad. (2013). 20, 819
doi: 10.1107/S0909049513025478
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An introductory overview to the special issue papers on diffraction structural biology in this issue of the journal.

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

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

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

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

J. Synchrotron Rad. (2013). 20, 838-842
doi: 10.1107/S0909049513020797
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The evolution of AR-NW12A into a multi-purpose end-station with optional high-pressure crystallography is described.

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

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

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

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

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

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

J. Synchrotron Rad. (2013). 20, 875-879
doi: 10.1107/S0909049513020700
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X-ray structure determination and deuteration of nattokinase were performed to facilitate neutron crystallographic analysis.

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

J. Synchrotron Rad. (2013). 20, 884-889
doi: 10.1107/S0909049513021110
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The crystal structure of endo-1,4-β-glucanase from the earthworm Eisenia fetida, which retained sufficient cellulase activity at low temperature, was determined at 1.5 Å resolution.

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

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

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

J. Synchrotron Rad. (2013). 20, 905-909
doi: 10.1107/S0909049513020736
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The Gly-rich loop of cyclin-dependent kinase 2 (CDK2) bound to TEI-I01800 as an MK2 specific inhibitor forms a β-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.

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

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

J. Synchrotron Rad. (2013). 20, 919-922
doi: 10.1107/S0909049513022772
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The present study analysed small-angle X-ray scattering profiles of myoglobin to examine how removal of the heme changes the intermolecular interaction.

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

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

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

J. Synchrotron Rad. (2013). 20, 938-942
doi: 10.1107/S0909049513022875
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The BL-17A macromolecular crystallography beamline at the Photon Factory was updated to improve the accuracy of diffraction experiments conducted using tiny crystals.

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

J. Synchrotron Rad. (2013). 20, 948-952
doi: 10.1107/S0909049513022887
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An online UV–visible microspectrophotometer has been developed for the macromolecular crystallography beamline at SPring-8. Details of this spectrophotometer are reported.

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

J. Synchrotron Rad. (2013). 20, 958-961
doi: 10.1107/S0909049513020815
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Fundamental trials to realise the proton polarization technique for detecting hydrogen with higher sensitivity in neutron protein crystallography are described.

J. Synchrotron Rad. (2013). 20, 962-967
doi: 10.1107/S0909049513020803
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The crystal structure of the complex between the C-terminal domain of Streptococcus pyogenes β-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.

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

J. Synchrotron Rad. (2013). 20, 974-979
doi: 10.1107/S0909049513020785
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The high-resolution crystal structure of the human CK2 catalytic subunit reveals the structural insights that probably promote drug discovery.

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

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

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

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

J. Synchrotron Rad. (2013). 20, 999-1002
doi: 10.1107/S0909049513021584
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A convenient gas-derivatization tool for protein crystals is presented in combination with a fine-needle capillary and a gas-pressure regulator.

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

current events

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