Journal of Synchrotron Radiation

Volume 15, Part 3 (May 2008)


2nd International Symposium on Diffraction Structural Biology (ISDSB2007)

Tower Hall Funabori, Tokyo, Japan, 10-13 September 2007

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


[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: The reaction centre for disulfide bond generation in E. coli, which is composed of DsbB (emerald ribbon) and ubiquinone (purple stick) (see Inaba, pages 199-201). The disulfide bond generated here (shown with yellow mesh) is transferred to downstream proteins oxidatively folding via DsbA, a primary disulfide-donating enzyme. (Figure produced by Kenji Inaba and Mamoru Suzuki.)

diffraction structural biology


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J. Synchrotron Rad. (2008). 15, 199-201  [ doi:10.1107/S090904950706061X ]

Protein disulfide bond generation in Escherichia coli DsbB-DsbA

K. Inaba

Synopsis: The crystal structure of the DsbB-DsbA-ubiquinone ternary complex has revealed a mechanism of protein disulfide bond generation in Escherichia coli.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 202-203  [ doi:10.1107/S0909049508000447 ]

Ultrahigh-resolution crystallography and related electron density and electrostatic properties in proteins

C. Lecomte, C. Jelsch, B. Guillot, B. Fournier and A. Lagoutte

Synopsis: Ultrahigh-resolution protein diffraction data allow valence electron density modelling and calculations of experimental electrostatic properties. Protein-ligand interaction energy may therefore be estimated.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 204-207  [ doi:10.1107/S0909049507064229 ]

Key steps in the structure-based optimization of the hepatitis C virus NS3/4A protease inhibitor SCH503034

V. Madison, A. J. Prongay, Z. Guo, N. Yao, J. Pichardo, T. Fischmann, C. Strickland, J. Myers Jr, P. C. Weber, B. M. Beyer, R. Ingram, Z. Hong, W. W. Prosise, L. Ramanathan, S. S. Taremi, T. Yarosh-Tomaine, R. Zhang, M. Senior, R.-S. Yang, B. Malcolm, A. Arasappan, F. Bennett, S. L. Bogen, K. Chen, E. Jao, Y.-T. Liu, R. G. Lovey, A. K. Saksena, S. Venkatraman, V. Girijavallabhan and F. G. Njoroge

Synopsis: Crystal structures of protease/inhibitor complexes guided optimization of the buried nonpolar surface area thereby maximizing hydrophobic binding. The resulting potent tripeptide inhibitor is in clinical trials.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 208-210  [ doi:10.1107/S090904950706846X ]

Structural studies on Helicobacter pylori ATP-dependent protease, FtsH

S. H. Kim, G. B. Kang, H.-E. Song, S. J. Park, M.-H. Bea and S. H. Eom

Synopsis: The crystal structures of the Helicobacter pylori FtsH ATPase domain in the nucleotide-free state and complexed with ADP have been determined.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 211-214  [ doi:10.1107/S0909049508004640 ]

Structure of six-transmembrane cation channels revealed by single-particle analysis from electron microscopic images

K. Mio, T. Ogura and C. Sato

Synopsis: Single-particle analysis is a computer-aided method for determining protein structure using projection images obtained by electron microscopy. Recently reconstructed 6-TM-type cation channels demonstrate the structural similarities and divergence of the family.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 215-218  [ doi:10.1107/S0909049508000824 ]

Protein structures by spallation neutron crystallography

P. Langan, Z. Fisher, A. Kovalevsky, M. Mustyakimov, A. Sutcliffe Valone, C. Unkefer, M. J. Waltman, L. Coates, P. D. Adams, P. V. Afonine, B. Bennett, C. Dealwis and B. P. Schoenborn

Synopsis: The capabilities of the Protein Crystallography Station at Los Alamos Neutron Science Center for determining protein structures by spallation neutron crystallography are illustrated, and the methodological and technological advances that are emerging from the Macromolecular Neutron Crystallography consortium are described.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 219-222  [ doi:10.1107/S0909049507066319 ]

Solution structures of RseA and its complex with RseB

K. S. Jin, D. Y. Kim, Y. Rho, V. B. Le, E. Kwon, K. K. Kim and M. Ree

Synopsis: Conformational changes of RseA and RseB were observed by circular dichroism and small-angle X-ray scattering upon the formation of their complex.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 223-226  [ doi:10.1107/S0909049507064813 ]

An optimal exposure strategy for cryoprotected virus crystals with lattice constants greater than 1000 Å

L. Gan and J. E. Johnson

Synopsis: Many supramolecular complexes form crystals that have lattice constants of the order of 1000 Å. An optimized method for data collection and processing is described.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 227-230  [ doi:10.1107/S090904950705666X ]

Fragment approaches in structure-based drug discovery

R. E. Hubbard

Synopsis: Fragment-based methods are successfully generating novel and selective drug-like inhibitors of protein targets, with a number of groups reporting compounds entering clinical trials. This paper summarizes the key features of the approach as one of the tools in structure-guided drug discovery.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 231-234  [ doi:10.1107/S0909049508003993 ]

Highly bright X-ray generator using heat of fusion with a specially designed rotating anticathode

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

Synopsis: A very compact X-ray generator, 4.3 times more brilliant than can be attained by a conventional rotating-anticathode X-ray generator, has been developed using a U-shaped rotating anticathode and a high-flux electron gun with focusing bending magnet.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 235-238  [ doi:10.1107/S0909049508003397 ]

High-resolution X-ray microdiffraction analysis of natural teeth

J. Xue, L. Zhang, L. Zou, Y. Liao, J. Li, L. Xiao and W. Li

Synopsis: In situ microzone X-ray diffraction analysis of natural teeth is presented. From our experiment, layer orientation and continuous crystal variations in teeth could be conveniently studied using fast online measurements by high-resolution X-ray microdiffraction equipment.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 239-242  [ doi:10.1107/S0909049507068586 ]

Interaction of HIV-1 aspartic protease with its inhibitor, by molecular dynamics and ab initio fragment molecular orbital method

K. Koyano and T. Nakano

Synopsis: Molecular dynamics and the ab initio fragment molecular orbital method were applied to investigate the interaction of HIV-1 aspartic protease with its inhibitor. The interaction energy of the inhibitor at the active sites of aspartic acid obtained by the ab initio fragment molecular orbital method was as great as 50 kcal mol-1, coinciding with a tetrahedral transition state.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 243-245  [ doi:10.1107/S0909049507054325 ]

Trimeric structure and conformational equilibrium of M-ficolin fibrinogen-like domain

M. Tanio, S. Kondo, S. Sugio and T. Kohno

Synopsis: The crystal structure and ligand-binding study of M-ficolin provides an insight into its discrimination mechanism between self and non-self.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 246-249  [ doi:10.1107/S0909049507062826 ]

A degradation signal recognition in prokaryotes

E. Y. Park and H. K. Song

Synopsis: Substrates tagged with ssrA are recognized and degraded by a subset of the Clp family, ATP-dependent proteases in prokaryotes. This paper describes the mechanism of intracellular breakdown of ssrA-tagged substrates by ClpXP and its adaptor protein, SspB.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 250-253  [ doi:10.1107/S0909049507064655 ]

Deduced catalytic mechanism of D-amino acid amidase from Ochrobactrum anthropi SV3

S. Okazaki, A. Suzuki, H. Komeda, Y. Asano and T. Yamane

Synopsis: The catalytic mechanism of D-amino acid amidase from Ochrobactrum anthropi SV3 has been deduced.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 254-257  [ doi:10.1107/S0909049507068471 ]

Novel dimer structure of a membrane-bound protease with a catalytic Ser-Lys dyad and its linkage to stomatin

H. Yokoyama, S. Hamamatsu, S. Fujii and I. Matsui

Synopsis: The crystal structure of the K138A mutant of the 1510-N protease specific for p-stomatin was determined at 2.3 Å resolution. The structure shows a novel dimer form, and the kinked L2 loop indicates that Lys138 would probably have an important effect on the conformation of L2.

PDB reference: 3bpp

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 258-261  [ doi:10.1107/S0909049507066769 ]

Performance of an electron gun for a high-brightness X-ray generator

T. Sugimura, S. Ohsawa and M. Ikeda

Synopsis: The development of an electron gun for a high-brightness X-ray generator whose target brilliance is 60 kW mm-2 is reported.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 262-265  [ doi:10.1107/S0909049507056531 ]

Crystal twinning of human MD-2 recognizing endotoxin cores of lipopolysaccharide

U. Ohto and Y. Satow

Synopsis: Twinned crystals of humaan MD-2 are transformed into single crystals with cryoprotectant optimization.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 266-268  [ doi:10.1107/S0909049507054799 ]

Crystallization of the Atg12-Atg5 conjugate bound to Atg16 by the free-interface diffusion method

N. N. Noda, Y. Fujioka, Y. Ohsumi and F. Inagaki

Synopsis: The Atg12-Atg5 conjugate was prepared by in vivo reconstitution and was crystallized with Atg16 using the free-interface diffusion method.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 269-272  [ doi:10.1107/S0909049508001842 ]

Protein crystallization in a 100 nl solution with new stirring equipment

S. Maki, R. Murai, H. Y. Yoshikawa, T. Kitatani, S. Nakata, H. Kawahara, H. Hasenaka, A. Kobayashi, S. Okada, S. Sugiyama, H. Adachi, H. Matsumura, K. Takano, S. Murakami, T. Inoue, T. Sasaki and Y. Mori

Synopsis: To investigate quantitatively the effects of stirring on protein crystallization, a new stirring system which can agitate a protein solution, ~100 nl, by providing Hagen-Poiseuille flow has been successfully developed.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 273-276  [ doi:10.1107/S090904950705114X ]

Structural insights into the similar modes of Nrf2 transcription factor recognition by the cytoplasmic repressor Keap1

B. Padmanabhan, K. I. Tong, A. Kobayashi, M. Yamamoto and S. Yokoyama

Synopsis: The structure of mouse Keap1-DC complexed with the DLG motif peptide of Nrf2 transcription factor was determined at 1.9 Å resolution. The structure showed that the peptide binds to Keap1-DC at the bottom region of the [beta]-propeller domain.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 277-280  [ doi:10.1107/S0909049507058979 ]

Hydrogen bonds of DsrD protein revealed by neutron crystallography

T. Chatake, Y. Higuchi, N. Mizuno, I. Tanaka, N. Niimura and Y. Morimoto

Synopsis: Hydrogen bonds of DNA-binding protein DsrD have been determined by neutron diffraction. In terms of proton donors and acceptors, DsrD protein shows striking differences from other proteins.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 281-284  [ doi:10.1107/S0909049508006584 ]

Development of an X-ray HARP-FEA detector system for high-throughput protein crystallography

T. Miyoshi, N. Igarashi, N. Matsugaki, Y. Yamada, K. Hirano, K. Hyodo, K. Tanioka, N. Egami, M. Namba, M. Kubota, T. Kawai and S. Wakatsuki

Synopsis: A new detector system for protein crystallography based on an X-ray HARP-FEA is presented.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 285-287  [ doi:10.1107/S0909049508004470 ]

Mutagenesis of the crystal contact of acidic fibroblast growth factor

E. Honjo, T. Tamada, M. Adachi, R. Kuroki, A. Meher and M. Blaber

Synopsis: Several mutations at Glu81 located on the crystal contact of human acidic fibroblast growth factor were studied in an effort to improve crystal growth. Mutation to Ser and Thr resulted in crystallization of a rather bulky form of the wild type, whereas mutation to Val prohibited crystallization. These results suggest that crystal growth may be controlled by designing a new interface by protein engineering.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 288-291  [ doi:10.1107/S0909049507064679 ]

Mail-in data collection at SPring-8 protein crystallography beamlines

N. Okazaki, K. Hasegawa, G. Ueno, H. Murakami, T. Kumasaka and M. Yamamoto

Synopsis: A mail-in data collection system at SPring-8, which is a web application with automated beamline operation, has been developed.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 292-295  [ doi:10.1107/S0909049507067118 ]

X-ray beam stabilization at BL-17A, the protein microcrystallography beamline of the Photon Factory

N. Igarashi, K. Ikuta, T. Miyoshi, N. Matsugaki, Y. Yamada, M. S. Yousef and S. Wakatsuki

Synopsis: BL-17A is a new structural biology beamline at the Photon Factory, dedicated to protein crystallography of microcrystals. Here the X-ray beam stabilization techniques used at BL-17A are described.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 296-299  [ doi:10.1107/S0909049508004019 ]

Implementation of remote monitoring and diffraction evaluation systems at the Photon Factory macromolecular crystallography beamlines

Y. Yamada, N. pHonda, N. Matsugaki, N. Igarashi, M. Hiraki and S. Wakatsuki

Synopsis: At the Photon Factory macromolecular crystallography beamlines, two new functions, remote monitoring and diffraction image evaluation, have been developed and installed on the beamline controlling system STARS (simple transmission and retrieval system).

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 300-303  [ doi:10.1107/S0909049507064680 ]

High-throughput operation of sample-exchange robots with double tongs at the Photon Factory beamlines

M. Hiraki, S. Watanabe, N. pHonda, Y. Yamada, N. Matsugaki, N. Igarashi, Y. Gaponov and S. Wakatsuki

Synopsis: Sample-exchange robots with a double-tongs system that could exchange samples within 10 s have been developed.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 304-307  [ doi:10.1107/S0909049508002458 ]

X-ray crystallographic and biochemical characterizations of a mutant photosystem II complex from Thermosynechococcus vulcanus with the psbTc gene inactivated by an insertion mutation

T. Henmi, M. Iwai, M. Ikeuchi, K. Kawakami, J.-R. Shen and N. Kamiya

Synopsis: The characterization of a PsbTc-truncated mutant photosystem II complex is described.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 308-311  [ doi:10.1107/S0909049507060670 ]

Complex of human neutrophil elastase with 1/2SLPI

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

Synopsis: The 1/2SLPI and HNE complex structure was solved at 1.7 Å resolution and compared with the interaction mechanism of elafin.

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 312-315  [ doi:10.1107/S0909049507059559 ]

Crystallization and evaluation of hen egg-white lysozyme crystals for protein pH titration in the crystalline state

W. Iwai, D. Yagi, T. Ishikawa, Y. Ohnishi, I. Tanaka and N. Niimura

Synopsis: Hen egg-white lysozyme was crystallized over a wide pH range (2.5-8.0) and the quality of the crystals was characterized. Crystallization phase diagrams at pH 2.5, 6.0 and 7.5 were determined

Online 18 April 2008


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J. Synchrotron Rad. (2008). 15, 316-318  [ doi:10.1107/S0909049507068598 ]

Effect of amino acids and amino acid derivatives on crystallization of hemoglobin and ribonuclease A

L. Ito, T. Kobayashi, K. Shiraki and H. Yamaguchi

Synopsis: The effect of the addition of amino acids and amino acid derivatives on the crystallization of hemoglobin and ribonuclease A has been evaluated. The results showed that certain types of additives expand the concentration conditions in which crystals are formed.

Online 18 April 2008


current events


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J. Synchrotron Rad. (2008). 15, 319-321  [ doi:10.1107/S0909049508009175 ]

Current events

Online 18 April 2008


 

J. Synchrotron Rad. (2008). 15, 322

forthcoming meetings and short courses


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