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Crystallographic data for soybean hydrophobic protein
J. Mol. Biol. (1989) 210, 235-236
Crystallographic Data for Soybean Hydrophobic Protein The soybean hydrophobic protein belongs to a family of proteins that contains a number of storage and phosphohpid binding proteins. Its function is not known, but its overall hydrophobic nature is typical of many membrane proteins of similar size. The molecular with a=52.01 A. weight is 8.3 x 103, and it crystallizes in the space group P2,2,2,, h = 43-50 A and c = 2880 A. Th e crystals diffract to I .%A resolution, and are thus suitable for X-ray structural studies.
b=43.50(3) A and c= 28.80(3) A (1 A=@1 nm) determined from diffractometer data. The molecular weight is 8.3 x 103, and the molecular volume estimated using standard volumes of residues (Chothia, 1975; Zamyatnin, 1972) is 10,300 A3. Consequently, the number of molecules per unit cell must be four, the solvent occupation factor around 37%, and the calculated density 1.21 g/cm3. The crystals diffract to a resolution of 1.8 A, and a trial diffractometer measurement using Mo radiation showed less than 3% degradation over a period of six days. Further recordings are being made with precession methods in a search for heavy-atom derivatives. Structural studies (Marion et al., unpublished results) have also been started on 9 x lo3 M, amino acid phospholipid transfer proteins from cereal (Tchang et al., 1988), and we hope that structural comparisons of the different proteins will add further details to our knowledge of t,heir function.
The function of the compound under investigation is not yet understood, but the analysis of its cnmposit,ion indicates strong hydrophobicity (Odani et al.: 1987). Tt is therefore of interest a priori to determine whether the hydrophobic part of the surface induces ordered arrangements of the water similar to those found in crambin (Teeter, 1984), and whether such arrangements might be of a more general nature. Recently, hydrophobic cluster analysis (Henrissat et al. 1 1988) has shown the protein to belong to a family of proteins, whose members are known to be either storage proteins or involved in phospholipid transfer. Its relatively low homology with the subgroups does not,, however, allow the conclusion to be drawn, that the protein has any of these functions, but work is being done to determine the strength of a putative proteinand to identify similar membrane interaction, proteins with known functions in other species (Marion. personal communication). The protein is easily extracted from soybean flour (Odani et al., 1987). It is only sparingly soluble in water, but’ can be dissolved in diluted acetic acid or 95:/, ethanol. The material used was extracted from the black Kuromame strain. Its sequence is known (Odani et al., 1987), and consists of a mixture of 78 and 80 residues. The difference is found at the N terminus, where in some cases two residues are missing. As the protein crystallizes spontaneously after extraction, it was decided not to separate the two species. but rather to accept a small eventual disorder at the location in question. Crysta.ls for diffraction studies were obtained using the hanging-drop method, and for this purpose the protein was dissolved in 1.25 M-acetic acid (30 mg/ml). The reservoir contained 90% (v/v) of a 1.1 M-ammonium acetate and 250 m&r-sodium chloride aqueous solution mixed with 10% (v/v) dioxane. The drop consisted of 2 ~1 of protein solution and 2 ~1 of the reservoir mixture, and crystals of dimension O-1 mm x @2 mm x 0.5 mm were formed within 24 hours. The space group is P212121, as observed on precession photographs. with a = 52.01(8) A, 0022-283s/s9/210235-02
$03.00/0
We are indebted to Dr C. Berthet, EMBL, for help with the diffraction work, to Dr R. Leberman, EMBL, for discussions on the aspects of protein homology a,nd to Dr P. Metcalf, EMBL, for useful information concerning crystal growth techniques.
Mogens Steen Lehmann’ Eva Pebay-Peyroula’ Claudine Cohen-Addad’a2 Shoji Odani3 ‘Institut Laue-Langevin Avenue des Martyrs BP 156X, 38042 Grenoble Cedex, France ‘Laboratoire Biologie Structurale. CNRS, Centre d’Etudes Nucleaires BP 85X, 38041 Grenoble Cedex, France 3Department of Biochemistry Niigata University School of Medicine Niigata, Japan Received
24 April
1989, a.nd in revised
form
URA
1333
13 June
1989
References Chothia, C. (1975). Nature (London), 254, 304-308. Henrissat, B., Popineau, Y. & Kader. J.-C. (1988). Rio&em. J. 255, 90-905.
235
0 1989 Academic Press Limited
M. S. Lehmann
Odani. S., Koide, T., Ono, T., Seto, Y. & Tanaka, T. (1987). Eur. J. Biochem. 162, 485-491. Tchang, F., This, P., Stiefel, V., Arondel, V., March, M.-D.. Pages, M., Puigdomenech, P., Grellet, F., Delseny, M., Bouillon, P., Huet, J.-C., Guerbette, F., Reauvais-Cante, F., Duranton, H., Pernollet, J.-C. &
et al.
Kader. J.-C. (1988). J. Biol. C:hm. 263, IWW 16855. Teeter, M. (1984). Proc. Nat. Acad. Sci., 1’S.A. 81. 6014 6018. Zamyatnin. A. A. (1972). Progr. Hioph,ys. Mol. Hiol. 24, 107-125.
Edited by R. Hu,ber
Crystallographic Data for Soybean Hydrophobic Protein The soybean hydrophobic protein belongs to a family of proteins that contains a number of storage and phosphohpid binding proteins. Its function is not known, but its overall hydrophobic nature is typical of many membrane proteins of similar size. The molecular with a=52.01 A. weight is 8.3 x 103, and it crystallizes in the space group P2,2,2,, h = 43-50 A and c = 2880 A. Th e crystals diffract to I .%A resolution, and are thus suitable for X-ray structural studies.
b=43.50(3) A and c= 28.80(3) A (1 A=@1 nm) determined from diffractometer data. The molecular weight is 8.3 x 103, and the molecular volume estimated using standard volumes of residues (Chothia, 1975; Zamyatnin, 1972) is 10,300 A3. Consequently, the number of molecules per unit cell must be four, the solvent occupation factor around 37%, and the calculated density 1.21 g/cm3. The crystals diffract to a resolution of 1.8 A, and a trial diffractometer measurement using Mo radiation showed less than 3% degradation over a period of six days. Further recordings are being made with precession methods in a search for heavy-atom derivatives. Structural studies (Marion et al., unpublished results) have also been started on 9 x lo3 M, amino acid phospholipid transfer proteins from cereal (Tchang et al., 1988), and we hope that structural comparisons of the different proteins will add further details to our knowledge of t,heir function.
The function of the compound under investigation is not yet understood, but the analysis of its cnmposit,ion indicates strong hydrophobicity (Odani et al.: 1987). Tt is therefore of interest a priori to determine whether the hydrophobic part of the surface induces ordered arrangements of the water similar to those found in crambin (Teeter, 1984), and whether such arrangements might be of a more general nature. Recently, hydrophobic cluster analysis (Henrissat et al. 1 1988) has shown the protein to belong to a family of proteins, whose members are known to be either storage proteins or involved in phospholipid transfer. Its relatively low homology with the subgroups does not,, however, allow the conclusion to be drawn, that the protein has any of these functions, but work is being done to determine the strength of a putative proteinand to identify similar membrane interaction, proteins with known functions in other species (Marion. personal communication). The protein is easily extracted from soybean flour (Odani et al., 1987). It is only sparingly soluble in water, but’ can be dissolved in diluted acetic acid or 95:/, ethanol. The material used was extracted from the black Kuromame strain. Its sequence is known (Odani et al., 1987), and consists of a mixture of 78 and 80 residues. The difference is found at the N terminus, where in some cases two residues are missing. As the protein crystallizes spontaneously after extraction, it was decided not to separate the two species. but rather to accept a small eventual disorder at the location in question. Crysta.ls for diffraction studies were obtained using the hanging-drop method, and for this purpose the protein was dissolved in 1.25 M-acetic acid (30 mg/ml). The reservoir contained 90% (v/v) of a 1.1 M-ammonium acetate and 250 m&r-sodium chloride aqueous solution mixed with 10% (v/v) dioxane. The drop consisted of 2 ~1 of protein solution and 2 ~1 of the reservoir mixture, and crystals of dimension O-1 mm x @2 mm x 0.5 mm were formed within 24 hours. The space group is P212121, as observed on precession photographs. with a = 52.01(8) A, 0022-283s/s9/210235-02
$03.00/0
We are indebted to Dr C. Berthet, EMBL, for help with the diffraction work, to Dr R. Leberman, EMBL, for discussions on the aspects of protein homology a,nd to Dr P. Metcalf, EMBL, for useful information concerning crystal growth techniques.
Mogens Steen Lehmann’ Eva Pebay-Peyroula’ Claudine Cohen-Addad’a2 Shoji Odani3 ‘Institut Laue-Langevin Avenue des Martyrs BP 156X, 38042 Grenoble Cedex, France ‘Laboratoire Biologie Structurale. CNRS, Centre d’Etudes Nucleaires BP 85X, 38041 Grenoble Cedex, France 3Department of Biochemistry Niigata University School of Medicine Niigata, Japan Received
24 April
1989, a.nd in revised
form
URA
1333
13 June
1989
References Chothia, C. (1975). Nature (London), 254, 304-308. Henrissat, B., Popineau, Y. & Kader. J.-C. (1988). Rio&em. J. 255, 90-905.
235
0 1989 Academic Press Limited
M. S. Lehmann
Odani. S., Koide, T., Ono, T., Seto, Y. & Tanaka, T. (1987). Eur. J. Biochem. 162, 485-491. Tchang, F., This, P., Stiefel, V., Arondel, V., March, M.-D.. Pages, M., Puigdomenech, P., Grellet, F., Delseny, M., Bouillon, P., Huet, J.-C., Guerbette, F., Reauvais-Cante, F., Duranton, H., Pernollet, J.-C. &
et al.
Kader. J.-C. (1988). J. Biol. C:hm. 263, IWW 16855. Teeter, M. (1984). Proc. Nat. Acad. Sci., 1’S.A. 81. 6014 6018. Zamyatnin. A. A. (1972). Progr. Hioph,ys. Mol. Hiol. 24, 107-125.
Edited by R. Hu,ber