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Acta Cryst. (2014). A70, C500
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Crystallization trial is one of the most important but time-consuming steps in macromolecular crystallography. Once a crystal appears in a certain crystallization condition, the crystal is typically harvested from the crystallization drop, soaked into a cryoprotection buffer, flash-cooled with a liquid nitrogen or cold gas flow and finally evaluated its diffraction quality by an X-ray beam. During these long process, crystal may be damaged and the result from the diffraction experiment does not necessarily reflect a nature of the crystal. On in-situ diffraction experiment, where a crystal in a crystallization drop is directly irradiated to an X-ray beam, a diffraction image from a crystal without any external factors such as harvesting and cryoprotection and, as a result, a nature of crystal can be evaluated quickly. In the Photon Factory, a new table-top diffractometer for in-situ diffraction experiments has been developed. It consists of XYZ translation stages with a plate handler, on-axis viewing system with a large numeric aperture and a plate rack where ten crystallization plates can be placed. These components sit on a common plate and it is placed on the existing diffractometer table in the beamline endstation. The CCD detector with a large active area and a pixel array detector with a small active area are used for acquiring diffraction images from crystals. Dedicated control software and user interface were also developed. Since 2014, user operation of the new diffractometer was started and in-situ diffraction experiments were mainly performed for evaluations of crystallization plates from a large crystallization screening project in our facility. BL-17A [1], one of micro-focus beamlines at the Photon Factory, is planned to be upgraded in March 2015. With this upgrade, a new diffractometer, which has a capability to handle a crystallization plate, will be installed so that diffraction data sets from crystals in crystallization drop can be collected.

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Acta Cryst. (2014). A70, C604
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Single wavelength anomalous diffraction (SAD) is a powerful experimental phasing technique used in macromolecular crystallography (MX). SAD is based on the absorption of X-rays by heavy atoms, which can be either incorporated into the protein (crystal) or naturally present in the structure, such as sulfur or metal ions. In particular, sulfur seems to be an attractive candidate for phasing, because most proteins contain a considerable number of S atoms. However, the K-absorption edge of sulfur is around 5.1 Å wavelength (2.4 keV), which is far from the optimal wavelength of most MX-beamlines at synchrotrons. Therefore, phasing experiments have to be performed further away from the absorption edge, which results in weaker anomalous signal. This explains why S-SAD was not commonly used for a long time, although its feasibility was illustrated by the ground-breaking study by Hendrickson and Teeter [1]. Recent developments in instrumentation, software and methodology made it possible to measure intensities more accurately, and, as a consequence, S-SAD has lately obtained more and more attention [2]. The beamline BL-1A at Photon factory (KEK, Japan) is designed to take full advantage of a long wavelength X-ray beam at around 3 Å to further enhance anomalous signals. We performed S-SAD experiments at BL-1A using two different wavelengths (1.9 Å and 2.7 Å) and compared their phasing capabilities. This methodological study was performed with ferredoxin reductase crystals of various sizes. In order to guarantee statistical validity and to exclude the influence of a particular sample, we repeated the comparison with several crystals. The novelty in the approach consists in using very long wavelengths (2.7 Å), not fully exploited in the literature so far. According to our study, the 2.7 Å wavelength shows - despite strong absorption effects of the diffracted X-rays - more successful phasing results than at 1.9 Å.

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Acta Cryst. (2014). A70, C608
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Sphingobium sp. SYK-6 grows on a lignin-related biphenyl compound as the sole carbon and energy source and was initially isolated from a pond waste liquor from a kraft pulp mill. In SYK-6, 5-CH3-H4folate is synthesized from aromatic compounds such as a vanillate by a O-demethylase, LigM. The 5-CH3-H4folate is then converted to 5,10-CH2-H4folate, which is utilized for syntheses of DNA, repair DNA, and methylate DNA as well as to act as a cofactor in certain biological reactions, by another enzyme, MetF. In other bacterial speceis, 5,10-CH2-H4folate is directly synthesized by T- and H-proteins that are enzymes in Glycine Cleavage System. It is considered that SYK-6 has evolved to acquire this unique pathway for the 5,10-CH2-H4folate production, in order to survive in extreme environmental condition. To elucidate the molecular mechanisim of this pathway, we have carried out the structural analysis of LigM. LigM was purified by using IMPACT system provided from NEB, which use intein and affinity chitin-binding tag. After crystallization screening, a reservoir solution of 0.2 M Mg acetate, 0.1 M Acetate buffer pH 4.6, and 20 %(w/v) PEG8000 gave a needle crystals with approximate dimensions of 0.3×0.1×0.01 mm3. A diffraction data set was collected with 1.1 Å wavelength at BL1-A in the Photon Factory. However, phasing trials via molecular replacement (using a model with 19% sequence identity) failed. Because LigM is a 53 kDa protein and contains fourteen sulfur atoms, LigM is an interesting candidate for SAD phasing with sulfur (S-SAD). Diffraction data sets of LigM crystals were collected with 1.9 and 2.7 Å wavelengths, reaching a maximum resolution of 2.3Å. Preliminary results are promising for solving the phase problem via S-SAD. This study is also of methodological interest as the phasing capability of two different wavelengths can be compared. A thorough analysis of the diffraction data is in progress.

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Acta Cryst. (2014). A70, C611
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Single-wavelength anomalous dispersion (SAD) experiment with light atoms as anomalous scatterers has been carried out using longer wavelengths up to 2.3 Å. We have been developing a synchrotron beamline dedicated to the SAD experiments where wavelengths longer than 2.7 Å are available to enhance weak anomalous signals. Larger background noise due to the longer wavelength, which is one of the major problems in the experiment, is reduced by introducing a standing helium chamber surrounding both the whole diffractometer and the X-ray detector. The system allows to perform experiments with normal and long waveldngths under the same environment. Helium cold stream is fed into the chamber at the sample position and reused after removing contaminants to keep the temperature of the stream at 30 K or below economically. Capillary-top-mount method [1] was improved to further reduce the background noise and to accommodate with smaller or needle-shape crystals. Several results on de-novo structural solutions with sulfur-SAD phasing will be reported in addition to the current performance of the beamline and its future plan.

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Acta Cryst. (2014). A70, C839
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CagA is known as a major bacterial virulence determinant from Helicobacter pylori and is critical for gastric cancer. Upon delivery into the gastric epithelial cells, CagA localizes to the inner leaflet of the plasma membrane and promiscuously interacts with host proteins such as PAR1b and SHP2. The CagA-PAR1-SHP2 complex potentiates oncogenic signaling. Biochemical and physicochemical analyses revealed that CagA is comprises a structured N-terminal region (residues 1-876) and an intrinsically disordered C-terminal region (residues 877-1186). To understand the structure and function relationship of CagA, we determined the crystal structure of the N-terminal region (residues 1-876) of CagA [1]. The N-terminal CagA is rich in α-helices and composed of three domains. Domain I (residues 24-221) is linked to domain II (residues 303-644) by a disordered loop with about 80 amino acid residues. Domain II has a basic patch composed of 14 lysine and 2 arginine residues. Biological experiments revealed that the basic patch mediates the CagA-phosphatidylserine interaction to localize the inner face of the plasma membrane. In addition, we found that C-terminal disordered region forms a lariat-like loop by the interaction between NBS (residues 645 - 824) and CBS (residues 998 - 1038) in the disordered C-terminal region. The formation of the lariat-like loop facilitates promiscuous interaction of CagA with target protein such as SHP2.

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Acta Cryst. (2014). A70, C1157
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Crystallization has been a bottleneck in protein crystallography. Major problems in protein crystallization are 1) to find crystallization conditions effectively at the initial crystallization screening and 2) to improve the reproducibility of protein crystallization. To overcome these problems, we have proposed some techniques such as the immediate observation method (1). Recently, we realized that films and precipitates of oxidized proteins hampered the crystal formation, leading to poor reproducibility of the crystallization. To avoid oxidation of proteins, we examined anaerobic crystallization in an anaerobic chamber. The anaerobic chamber (Anaerobic `HARD', Hirasawa) was designed to carry out controlled anaerobic experiments for electron-transfer proteins. We have so far established typical procedures for the anaerobic crystallization (2). On the basis of our earlier experiences, the anaerobic crystallization was tested for various proteins. We found obvious differences between aerobic and anaerobic crystallization in some cases; some proteins could crystallize only under anaerobic conditions. Furthermore, the anaerobic crystallization improved reproducibility of crystallization as expected. We will report some examples of the anaerobic crystallization.
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