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Journal logoJOURNAL OF
SYNCHROTRON
RADIATION
ISSN: 1600-5775

May 2008 issue

2nd International Symposium on Diffraction Structural Biology (ISDSB2007)

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

Highlighted 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.)

facility information


diffraction structural biology


J. Synchrotron Rad. (2008). 15, 199-201
, https://doi.org/10.1107/S090904950706061X
link to html
The crystal structure of the DsbB–DsbA–ubiquinone ternary complex has revealed a mechanism of protein disulfide bond generation in Escherichia coli.

J. Synchrotron Rad. (2008). 15, 202-203
, https://doi.org/10.1107/S0909049508000447
link to html
Ultrahigh-resolution protein diffraction data allow valence electron density modelling and calculations of experimental electrostatic properties. Protein–ligand interaction energy may therefore be estimated.

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

J. Synchrotron Rad. (2008). 15, 208-210
, https://doi.org/10.1107/S090904950706846X
link to html
The crystal structures of the Helicobacter pylori FtsH ATPase domain in the nucleotide-free state and complexed with ADP have been determined.

J. Synchrotron Rad. (2008). 15, 211-214
, https://doi.org/10.1107/S0909049508004640
link to html
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.

J. Synchrotron Rad. (2008). 15, 215-218
, https://doi.org/10.1107/S0909049508000824
link to html
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.

J. Synchrotron Rad. (2008). 15, 219-222
, https://doi.org/10.1107/S0909049507066319
link to html
Conformational changes of RseA and RseB were observed by circular dichroism and small-angle X-ray scattering upon the formation of their complex.

J. Synchrotron Rad. (2008). 15, 223-226
, https://doi.org/10.1107/S0909049507064813
link to html
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.

J. Synchrotron Rad. (2008). 15, 227-230
, https://doi.org/10.1107/S090904950705666X
link to html
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.

J. Synchrotron Rad. (2008). 15, 231-234
, https://doi.org/10.1107/S0909049508003993
link to html
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.

J. Synchrotron Rad. (2008). 15, 235-238
, https://doi.org/10.1107/S0909049508003397
link to html
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.

J. Synchrotron Rad. (2008). 15, 239-242
, https://doi.org/10.1107/S0909049507068586
link to html
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.

J. Synchrotron Rad. (2008). 15, 243-245
, https://doi.org/10.1107/S0909049507054325
link to html
The crystal structure and ligand-binding study of M-ficolin provides an insight into its discrimination mechanism between self and non-self.

J. Synchrotron Rad. (2008). 15, 246-249
, https://doi.org/10.1107/S0909049507062826
link to html
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.

J. Synchrotron Rad. (2008). 15, 250-253
, https://doi.org/10.1107/S0909049507064655
link to html
The catalytic mechanism of D-amino acid amidase from Ochrobactrum anthropi SV3 has been deduced.

J. Synchrotron Rad. (2008). 15, 254-257
, https://doi.org/10.1107/S0909049507068471
link to html
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.

J. Synchrotron Rad. (2008). 15, 258-261
, https://doi.org/10.1107/S0909049507066769
link to html
The development of an electron gun for a high-brightness X-ray generator whose target brilliance is 60 kW mm−2 is reported.

J. Synchrotron Rad. (2008). 15, 262-265
, https://doi.org/10.1107/S0909049507056531
link to html
Twinned crystals of humaan MD-2 are transformed into single crystals with cryoprotectant optimization.

J. Synchrotron Rad. (2008). 15, 266-268
, https://doi.org/10.1107/S0909049507054799
link to html
The Atg12–Atg5 conjugate was prepared by in vivo reconstitution and was crystallized with Atg16 using the free-interface diffusion method.

J. Synchrotron Rad. (2008). 15, 269-272
, https://doi.org/10.1107/S0909049508001842
link to html
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.

J. Synchrotron Rad. (2008). 15, 273-276
, https://doi.org/10.1107/S090904950705114X
link to html
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 β-propeller domain.

J. Synchrotron Rad. (2008). 15, 277-280
, https://doi.org/10.1107/S0909049507058979
link to html
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.

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

J. Synchrotron Rad. (2008). 15, 285-287
, https://doi.org/10.1107/S0909049508004470
link to html
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.

J. Synchrotron Rad. (2008). 15, 288-291
, https://doi.org/10.1107/S0909049507064679
link to html
A mail-in data collection system at SPring-8, which is a web application with automated beamline operation, has been developed.

J. Synchrotron Rad. (2008). 15, 292-295
, https://doi.org/10.1107/S0909049507067118
link to html
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.

J. Synchrotron Rad. (2008). 15, 296-299
, https://doi.org/10.1107/S0909049508004019
link to html
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).

J. Synchrotron Rad. (2008). 15, 300-303
, https://doi.org/10.1107/S0909049507064680
link to html
Sample-exchange robots with a double-tongs system that could exchange samples within 10 s have been developed.


J. Synchrotron Rad. (2008). 15, 308-311
, https://doi.org/10.1107/S0909049507060670
link to html
The 1/2SLPI and HNE complex structure was solved at 1.7 Å resolution and compared with the interaction mechanism of elafin.

J. Synchrotron Rad. (2008). 15, 312-315
, https://doi.org/10.1107/S0909049507059559
link to html
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

J. Synchrotron Rad. (2008). 15, 316-318
, https://doi.org/10.1107/S0909049507068598
link to html
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.

current events


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

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