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note
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The T. thermophilus lleRS gene was cloned into a T7 polymerase expression vector and was overexpressed in E. coli strain JM109(DE3) (S. Fukai et al., in preparation). The recombinant protein was purified by a combination of heat treatment, anion-exchange chromatography, and reversed-phase fast performance liquid chromatography. Crystals were grown at 20°C by the hanging-drop vapor diffusion method (protein concentration of 20 mg/ml) against a reservoir solution containing 12% polyethylene glycol 4000, 6% isopropanol, 1% 2-methyl-pentane-2,4-diol, and 60 mM Hepes (pH 7.5). Two mutant proteins, with substitutions of Cys for Ala or Lys, were expressed, purified, and used for the preparation of mercury derivatives. Furthermore, we incorporated selenium into the lleRS by preparing the lleRS from the E. coli Met-auxotroph B834 strain cultured in the presence of selenomethionine. Crystals of the Cys- and selenomethionine-substituted proteins were grown by cross seeding. Heavy atom derivatives were prepared by cocrystallization of the Cys mutants and methylmercurichloride. Native and heavy atom derivative data were collected to 2.5 Å with a Weissenberg camera for macromolecules installed on the beam line 6A2 at the Photon Factory (Tsukuba, Japan). The data set for crystal of selenomethionine-substituted lleRS was collected inhouse on a Raxis-llc (Rigaku, Tokyo, Japan) image plate detector mounted on a Rigaku x-ray source. All of the data were processed with the DENZO and SCALEPACK programs (25). Subsequent calculations were carried out with the CCP4 program suite (26). Initial mercury sites in the derivative of the K3C mutant were determined with the RSPS program (26) from an isomorphous difference Patterson map. The phases from the mercury derivative were used to locate the positions of other mercury and selenium atoms by difference Fourier analysis. Heavy-atom parameters were refined with the MLPHARE (26) program. The overall figure of merit from 50 to 3.0 Å resolution is 0.74. After density modification with solvent flattening and histogram matching in the program DM (26) and solvent flipping in the SOLOMON (27) program, the atomic model of residues 1 to 818 could be built with the program O (28). Crystallographic positional and slow-cooling refinement was carried out with X-PLOR (29). The Ramaohandran plot analysis with the PROCHECK (30) program showed that 98.2% of the residues in the present structure are in the most favorable and the additionally allowed regions. We obtained the lle and Val complexes by transferring the crystals to a harvest buffer containing 10 mM amino acid substrates. The data sets were collected on a Raxis-llc image plate detector. After rigid-body refinement in the program AMORE (26), the R factors were reduced.
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2642688400
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unpublished data
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S. Fukai et al., unpublished data.
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Fukai, S.1
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18
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2642666284
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O. Nureki et al., data not shown
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O. Nureki et al., data not shown.
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20
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unpublished data
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O. Nureki et al., unpublished data.
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Nureki, O.1
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2642691482
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note
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2, and pyrophosphatase (5 μg/ml). Each time point was quenched in 1.25 ml of a solution of 2 mM sodium pyrophosphate, 8% activated charcoal, 1.4% perchloric acid, and 0.4% hydrochloric acid. After 10 min at room temperature, the charcoal was pelleted by centrifugation, and the phosphate content of 500 μl of each supernatant was quantitated by scintillation.
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25
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0031000512
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39
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2642606162
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note
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We thank M. Nakasako, N. Kamiya, M. Yamamoto, H. Iwasaki, T. Ueki, and Y. Maeda for data collection and helpful discussions; N. Watanabe and N. Sakabe for help with synchrotron data collection at the Tsukuba Photon Factory; and K. Nagai and A. Murzin for helpful comments. Supported in part by Grants-in-Aid for Scientific Research on Priority Areas (04272103 and 09278102) to S.Y. from the Ministry of Education, Science, Culture, and Sports of Japan and by grant GM15539 to P.S. and T.H. from NIH. T.H. is an NIH Postdoctoral Fellow. The coordinates for T. thermophilus lleRS have been deposited in the Brookhaven Protein Data Base (1ILE).
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