Crystal structure of the catalytic domain of human plasmin complexed with streptokinase

Science

Volumn 281, Issue 5383, 1998, Pages 1662-1668

  Wang, Xiaoqiang ^a   Lin, Xinli ^a   Loy, Jeffrey A ^a   Tang, Jordan ^a   Zhang, Xuejun C ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

PLASMIN; PLASMINOGEN; STREPTOKINASE;

ARTICLE; BLOOD CLOTTING; BLOOD CLOTTING DISORDER; CRYSTAL STRUCTURE; DRUG PROTEIN BINDING; ENZYME ACTIVATION; ENZYME ACTIVE SITE; FIBRIN CLOT; HYDROLYSIS; PRIORITY JOURNAL; PROTEIN DOMAIN;

BINDING SITES; CRYSTALLOGRAPHY, X-RAY; HUMANS; HYDROGEN BONDING; MODELS, MOLECULAR; PLASMIN; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT PROTEINS; STREPTOKINASE;

EID: 0032508547     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.281.5383.1662     Document Type: Article

References (50)

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16. 1, with cell parameters of a = 80.0 Å, b = 125.1 Å, c = 86.8 Å, and β = 105.4°. One crystallographic asymmetric unit contains two essentially identical SK-μPm complexes.
17. 562. The correct activation cleavage specificity in μPlg suggests that a low level of proteolytic activity had been restored from the low incidence of ribosome translation error [P. Schimmel, Acc. Chem. Res. 22, 232 (1989); X. L. Lin, M. Fusek, J. Tang, Adv. Exp. Med. Biol. 306, 255 (1991)].
18. 562. The correct activation cleavage specificity in μPlg suggests that a low level of proteolytic activity had been restored from the low incidence of ribosome translation error [P. Schimmel, Acc. Chem. Res. 22, 232 (1989); X. L. Lin, M. Fusek, J. Tang, Adv. Exp. Med. Biol. 306, 255 (1991)].
19. Diffraction data were collected on a Siemens area detector at room temperature. Molecular replacement with chymotrypsin [M. Harel, C. T. Su, F. Frolow, I. Silman, J. L. Sussman, Biochemistry 30, 5217 (1991)] as a search model established a local twofold symmetry. The MIR phases were solved with the programs SOLVE [T. C. Terwilliger and J. Berendzen, Acta Crystallogr. D 52, 749 (1996)] and MLPHARE [Z. Otwinowsky, in Isomorphous Replacement and Anomalous Scattering, Proceedings of the CCP4 Study Weekend, W. Wolf, P. R. Evans, A. G. W. Leslie, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1991), pp. 80-86] (see Table 1). The initial MIR phases were improved by electron density averaging over the twofold noncrystallographic symmetry and solvent flattening with the program DM [K. D. Cowtan and P. Main, Acta Crystallogr. D 52, 43 (1996)]. Model building from the electron density map was done with the program O [T. A. Jones, J. Y. Zou, S. W. Cowan, M. Kjelgaard, Acta Crystallogr. A 47, 110 (1991)]. The program SigmaA [R. J. Read, ibid. 42, 140 (1986)] was used to combine phase information at initial stages of model building. Refinement was carried out with the program X-PLOR version 3.8 [A. T. Brünger, J. Kuriyan, M. Karplus, Science 235, 458 (1987)]. Noncrystallographic-symmetry constraints were used throughout the refinement. At late stages of the refinement, both grouped temperature factor refinement and a bulk solvent correction were applied. The final R factor is 21.5% over the 20.0 to 2.9 Å resolution shell (29,980 reflections), and the free R [A. T. Brünger, Nature 355, 472 (1992)] is 29.2% (3330 reflections). Bond and angle deviations are 0.009 Å and 1.57°, respectively. Structural superposition and solvent-accessible surface calculation were carried out with the program EDPDB [X. Zhang and B. W. Matthews, J. Appl. Crystallogr. 28, 624 (1995)]. Figures in this manuscript were created with MOLSCRIPT and RASTER3D [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991); E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D 50, 869 (1994)]. The coordinates of the complex have been deposited in the Brookhaven Protein Databank (1BML).
20. Diffraction data were collected on a Siemens area detector at room temperature. Molecular replacement with chymotrypsin [M. Harel, C. T. Su, F. Frolow, I. Silman, J. L. Sussman, Biochemistry 30, 5217 (1991)] as a search model established a local twofold symmetry. The MIR phases were solved with the programs SOLVE [T. C. Terwilliger and J. Berendzen, Acta Crystallogr. D 52, 749 (1996)] and MLPHARE [Z. Otwinowsky, in Isomorphous Replacement and Anomalous Scattering, Proceedings of the CCP4 Study Weekend, W. Wolf, P. R. Evans, A. G. W. Leslie, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1991), pp. 80-86] (see Table 1). The initial MIR phases were improved by electron density averaging over the twofold noncrystallographic symmetry and solvent flattening with the program DM [K. D. Cowtan and P. Main, Acta Crystallogr. D 52, 43 (1996)]. Model building from the electron density map was done with the program O [T. A. Jones, J. Y. Zou, S. W. Cowan, M. Kjelgaard, Acta Crystallogr. A 47, 110 (1991)]. The program SigmaA [R. J. Read, ibid. 42, 140 (1986)] was used to combine phase information at initial stages of model building. Refinement was carried out with the program X-PLOR version 3.8 [A. T. Brünger, J. Kuriyan, M. Karplus, Science 235, 458 (1987)]. Noncrystallographic-symmetry constraints were used throughout the refinement. At late stages of the refinement, both grouped temperature factor refinement and a bulk solvent correction were applied. The final R factor is 21.5% over the 20.0 to 2.9 Å resolution shell (29,980 reflections), and the free R [A. T. Brünger, Nature 355, 472 (1992)] is 29.2% (3330 reflections). Bond and angle deviations are 0.009 Å and 1.57°, respectively. Structural superposition and solvent-accessible surface calculation were carried out with the program EDPDB [X. Zhang and B. W. Matthews, J. Appl. Crystallogr. 28, 624 (1995)]. Figures in this manuscript were created with MOLSCRIPT and RASTER3D [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991); E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D 50, 869 (1994)]. The coordinates of the complex have been deposited in the Brookhaven Protein Databank (1BML).
21. Diffraction data were collected on a Siemens area detector at room temperature. Molecular replacement with chymotrypsin [M. Harel, C. T. Su, F. Frolow, I. Silman, J. L. Sussman, Biochemistry 30, 5217 (1991)] as a search model established a local twofold symmetry. The MIR phases were solved with the programs SOLVE [T. C. Terwilliger and J. Berendzen, Acta Crystallogr. D 52, 749 (1996)] and MLPHARE [Z. Otwinowsky, in Isomorphous Replacement and Anomalous Scattering, Proceedings of the CCP4 Study Weekend, W. Wolf, P. R. Evans, A. G. W. Leslie, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1991), pp. 80-86] (see Table 1). The initial MIR phases were improved by electron density averaging over the twofold noncrystallographic symmetry and solvent flattening with the program DM [K. D. Cowtan and P. Main, Acta Crystallogr. D 52, 43 (1996)]. Model building from the electron density map was done with the program O [T. A. Jones, J. Y. Zou, S. W. Cowan, M. Kjelgaard, Acta Crystallogr. A 47, 110 (1991)]. The program SigmaA [R. J. Read, ibid. 42, 140 (1986)] was used to combine phase information at initial stages of model building. Refinement was carried out with the program X-PLOR version 3.8 [A. T. Brünger, J. Kuriyan, M. Karplus, Science 235, 458 (1987)]. Noncrystallographic-symmetry constraints were used throughout the refinement. At late stages of the refinement, both grouped temperature factor refinement and a bulk solvent correction were applied. The final R factor is 21.5% over the 20.0 to 2.9 Å resolution shell (29,980 reflections), and the free R [A. T. Brünger, Nature 355, 472 (1992)] is 29.2% (3330 reflections). Bond and angle deviations are 0.009 Å and 1.57°, respectively. Structural superposition and solvent-accessible surface calculation were carried out with the program EDPDB [X. Zhang and B. W. Matthews, J. Appl. Crystallogr. 28, 624 (1995)]. Figures in this manuscript were created with MOLSCRIPT and RASTER3D [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991); E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D 50, 869 (1994)]. The coordinates of the complex have been deposited in the Brookhaven Protein Databank (1BML).
22. Diffraction data were collected on a Siemens area detector at room temperature. Molecular replacement with chymotrypsin [M. Harel, C. T. Su, F. Frolow, I. Silman, J. L. Sussman, Biochemistry 30, 5217 (1991)] as a search model established a local twofold symmetry. The MIR phases were solved with the programs SOLVE [T. C. Terwilliger and J. Berendzen, Acta Crystallogr. D 52, 749 (1996)] and MLPHARE [Z. Otwinowsky, in Isomorphous Replacement and Anomalous Scattering, Proceedings of the CCP4 Study Weekend, W. Wolf, P. R. Evans, A. G. W. Leslie, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1991), pp. 80-86] (see Table 1). The initial MIR phases were improved by electron density averaging over the twofold noncrystallographic symmetry and solvent flattening with the program DM [K. D. Cowtan and P. Main, Acta Crystallogr. D 52, 43 (1996)]. Model building from the electron density map was done with the program O [T. A. Jones, J. Y. Zou, S. W. Cowan, M. Kjelgaard, Acta Crystallogr. A 47, 110 (1991)]. The program SigmaA [R. J. Read, ibid. 42, 140 (1986)] was used to combine phase information at initial stages of model building. Refinement was carried out with the program X-PLOR version 3.8 [A. T. Brünger, J. Kuriyan, M. Karplus, Science 235, 458 (1987)]. Noncrystallographic-symmetry constraints were used throughout the refinement. At late stages of the refinement, both grouped temperature factor refinement and a bulk solvent correction were applied. The final R factor is 21.5% over the 20.0 to 2.9 Å resolution shell (29,980 reflections), and the free R [A. T. Brünger, Nature 355, 472 (1992)] is 29.2% (3330 reflections). Bond and angle deviations are 0.009 Å and 1.57°, respectively. Structural superposition and solvent-accessible surface calculation were carried out with the program EDPDB [X. Zhang and B. W. Matthews, J. Appl. Crystallogr. 28, 624 (1995)]. Figures in this manuscript were created with MOLSCRIPT and RASTER3D [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991); E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D 50, 869 (1994)]. The coordinates of the complex have been deposited in the Brookhaven Protein Databank (1BML).
23. Diffraction data were collected on a Siemens area detector at room temperature. Molecular replacement with chymotrypsin [M. Harel, C. T. Su, F. Frolow, I. Silman, J. L. Sussman, Biochemistry 30, 5217 (1991)] as a search model established a local twofold symmetry. The MIR phases were solved with the programs SOLVE [T. C. Terwilliger and J. Berendzen, Acta Crystallogr. D 52, 749 (1996)] and MLPHARE [Z. Otwinowsky, in Isomorphous Replacement and Anomalous Scattering, Proceedings of the CCP4 Study Weekend, W. Wolf, P. R. Evans, A. G. W. Leslie, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1991), pp. 80-86] (see Table 1). The initial MIR phases were improved by electron density averaging over the twofold noncrystallographic symmetry and solvent flattening with the program DM [K. D. Cowtan and P. Main, Acta Crystallogr. D 52, 43 (1996)]. Model building from the electron density map was done with the program O [T. A. Jones, J. Y. Zou, S. W. Cowan, M. Kjelgaard, Acta Crystallogr. A 47, 110 (1991)]. The program SigmaA [R. J. Read, ibid. 42, 140 (1986)] was used to combine phase information at initial stages of model building. Refinement was carried out with the program X-PLOR version 3.8 [A. T. Brünger, J. Kuriyan, M. Karplus, Science 235, 458 (1987)]. Noncrystallographic-symmetry constraints were used throughout the refinement. At late stages of the refinement, both grouped temperature factor refinement and a bulk solvent correction were applied. The final R factor is 21.5% over the 20.0 to 2.9 Å resolution shell (29,980 reflections), and the free R [A. T. Brünger, Nature 355, 472 (1992)] is 29.2% (3330 reflections). Bond and angle deviations are 0.009 Å and 1.57°, respectively. Structural superposition and solvent-accessible surface calculation were carried out with the program EDPDB [X. Zhang and B. W. Matthews, J. Appl. Crystallogr. 28, 624 (1995)]. Figures in this manuscript were created with MOLSCRIPT and RASTER3D [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991); E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D 50, 869 (1994)]. The coordinates of the complex have been deposited in the Brookhaven Protein Databank (1BML).
24. Diffraction data were collected on a Siemens area detector at room temperature. Molecular replacement with chymotrypsin [M. Harel, C. T. Su, F. Frolow, I. Silman, J. L. Sussman, Biochemistry 30, 5217 (1991)] as a search model established a local twofold symmetry. The MIR phases were solved with the programs SOLVE [T. C. Terwilliger and J. Berendzen, Acta Crystallogr. D 52, 749 (1996)] and MLPHARE [Z. Otwinowsky, in Isomorphous Replacement and Anomalous Scattering, Proceedings of the CCP4 Study Weekend, W. Wolf, P. R. Evans, A. G. W. Leslie, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1991), pp. 80-86] (see Table 1). The initial MIR phases were improved by electron density averaging over the twofold noncrystallographic symmetry and solvent flattening with the program DM [K. D. Cowtan and P. Main, Acta Crystallogr. D 52, 43 (1996)]. Model building from the electron density map was done with the program O [T. A. Jones, J. Y. Zou, S. W. Cowan, M. Kjelgaard, Acta Crystallogr. A 47, 110 (1991)]. The program SigmaA [R. J. Read, ibid. 42, 140 (1986)] was used to combine phase information at initial stages of model building. Refinement was carried out with the program X-PLOR version 3.8 [A. T. Brünger, J. Kuriyan, M. Karplus, Science 235, 458 (1987)]. Noncrystallographic-symmetry constraints were used throughout the refinement. At late stages of the refinement, both grouped temperature factor refinement and a bulk solvent correction were applied. The final R factor is 21.5% over the 20.0 to 2.9 Å resolution shell (29,980 reflections), and the free R [A. T. Brünger, Nature 355, 472 (1992)] is 29.2% (3330 reflections). Bond and angle deviations are 0.009 Å and 1.57°, respectively. Structural superposition and solvent-accessible surface calculation were carried out with the program EDPDB [X. Zhang and B. W. Matthews, J. Appl. Crystallogr. 28, 624 (1995)]. Figures in this manuscript were created with MOLSCRIPT and RASTER3D [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991); E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D 50, 869 (1994)]. The coordinates of the complex have been deposited in the Brookhaven Protein Databank (1BML).
25. Diffraction data were collected on a Siemens area detector at room temperature. Molecular replacement with chymotrypsin [M. Harel, C. T. Su, F. Frolow, I. Silman, J. L. Sussman, Biochemistry 30, 5217 (1991)] as a search model established a local twofold symmetry. The MIR phases were solved with the programs SOLVE [T. C. Terwilliger and J. Berendzen, Acta Crystallogr. D 52, 749 (1996)] and MLPHARE [Z. Otwinowsky, in Isomorphous Replacement and Anomalous Scattering, Proceedings of the CCP4 Study Weekend, W. Wolf, P. R. Evans, A. G. W. Leslie, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1991), pp. 80-86] (see Table 1). The initial MIR phases were improved by electron density averaging over the twofold noncrystallographic symmetry and solvent flattening with the program DM [K. D. Cowtan and P. Main, Acta Crystallogr. D 52, 43 (1996)]. Model building from the electron density map was done with the program O [T. A. Jones, J. Y. Zou, S. W. Cowan, M. Kjelgaard, Acta Crystallogr. A 47, 110 (1991)]. The program SigmaA [R. J. Read, ibid. 42, 140 (1986)] was used to combine phase information at initial stages of model building. Refinement was carried out with the program X-PLOR version 3.8 [A. T. Brünger, J. Kuriyan, M. Karplus, Science 235, 458 (1987)]. Noncrystallographic-symmetry constraints were used throughout the refinement. At late stages of the refinement, both grouped temperature factor refinement and a bulk solvent correction were applied. The final R factor is 21.5% over the 20.0 to 2.9 Å resolution shell (29,980 reflections), and the free R [A. T. Brünger, Nature 355, 472 (1992)] is 29.2% (3330 reflections). Bond and angle deviations are 0.009 Å and 1.57°, respectively. Structural superposition and solvent-accessible surface calculation were carried out with the program EDPDB [X. Zhang and B. W. Matthews, J. Appl. Crystallogr. 28, 624 (1995)]. Figures in this manuscript were created with MOLSCRIPT and RASTER3D [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991); E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D 50, 869 (1994)]. The coordinates of the complex have been deposited in the Brookhaven Protein Databank (1BML).
26. Diffraction data were collected on a Siemens area detector at room temperature. Molecular replacement with chymotrypsin [M. Harel, C. T. Su, F. Frolow, I. Silman, J. L. Sussman, Biochemistry 30, 5217 (1991)] as a search model established a local twofold symmetry. The MIR phases were solved with the programs SOLVE [T. C. Terwilliger and J. Berendzen, Acta Crystallogr. D 52, 749 (1996)] and MLPHARE [Z. Otwinowsky, in Isomorphous Replacement and Anomalous Scattering, Proceedings of the CCP4 Study Weekend, W. Wolf, P. R. Evans, A. G. W. Leslie, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1991), pp. 80-86] (see Table 1). The initial MIR phases were improved by electron density averaging over the twofold noncrystallographic symmetry and solvent flattening with the program DM [K. D. Cowtan and P. Main, Acta Crystallogr. D 52, 43 (1996)]. Model building from the electron density map was done with the program O [T. A. Jones, J. Y. Zou, S. W. Cowan, M. Kjelgaard, Acta Crystallogr. A 47, 110 (1991)]. The program SigmaA [R. J. Read, ibid. 42, 140 (1986)] was used to combine phase information at initial stages of model building. Refinement was carried out with the program X-PLOR version 3.8 [A. T. Brünger, J. Kuriyan, M. Karplus, Science 235, 458 (1987)]. Noncrystallographic-symmetry constraints were used throughout the refinement. At late stages of the refinement, both grouped temperature factor refinement and a bulk solvent correction were applied. The final R factor is 21.5% over the 20.0 to 2.9 Å resolution shell (29,980 reflections), and the free R [A. T. Brünger, Nature 355, 472 (1992)] is 29.2% (3330 reflections). Bond and angle deviations are 0.009 Å and 1.57°, respectively. Structural superposition and solvent-accessible surface calculation were carried out with the program EDPDB [X. Zhang and B. W. Matthews, J. Appl. Crystallogr. 28, 624 (1995)]. Figures in this manuscript were created with MOLSCRIPT and RASTER3D [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991); E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D 50, 869 (1994)]. The coordinates of the complex have been deposited in the Brookhaven Protein Databank (1BML).
27. Diffraction data were collected on a Siemens area detector at room temperature. Molecular replacement with chymotrypsin [M. Harel, C. T. Su, F. Frolow, I. Silman, J. L. Sussman, Biochemistry 30, 5217 (1991)] as a search model established a local twofold symmetry. The MIR phases were solved with the programs SOLVE [T. C. Terwilliger and J. Berendzen, Acta Crystallogr. D 52, 749 (1996)] and MLPHARE [Z. Otwinowsky, in Isomorphous Replacement and Anomalous Scattering, Proceedings of the CCP4 Study Weekend, W. Wolf, P. R. Evans, A. G. W. Leslie, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1991), pp. 80-86] (see Table 1). The initial MIR phases were improved by electron density averaging over the twofold noncrystallographic symmetry and solvent flattening with the program DM [K. D. Cowtan and P. Main, Acta Crystallogr. D 52, 43 (1996)]. Model building from the electron density map was done with the program O [T. A. Jones, J. Y. Zou, S. W. Cowan, M. Kjelgaard, Acta Crystallogr. A 47, 110 (1991)]. The program SigmaA [R. J. Read, ibid. 42, 140 (1986)] was used to combine phase information at initial stages of model building. Refinement was carried out with the program X-PLOR version 3.8 [A. T. Brünger, J. Kuriyan, M. Karplus, Science 235, 458 (1987)]. Noncrystallographic-symmetry constraints were used throughout the refinement. At late stages of the refinement, both grouped temperature factor refinement and a bulk solvent correction were applied. The final R factor is 21.5% over the 20.0 to 2.9 Å resolution shell (29,980 reflections), and the free R [A. T. Brünger, Nature 355, 472 (1992)] is 29.2% (3330 reflections). Bond and angle deviations are 0.009 Å and 1.57°, respectively. Structural superposition and solvent-accessible surface calculation were carried out with the program EDPDB [X. Zhang and B. W. Matthews, J. Appl. Crystallogr. 28, 624 (1995)]. Figures in this manuscript were created with MOLSCRIPT and RASTER3D [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991); E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D 50, 869 (1994)]. The coordinates of the complex have been deposited in the Brookhaven Protein Databank (1BML).
28. Diffraction data were collected on a Siemens area detector at room temperature. Molecular replacement with chymotrypsin [M. Harel, C. T. Su, F. Frolow, I. Silman, J. L. Sussman, Biochemistry 30, 5217 (1991)] as a search model established a local twofold symmetry. The MIR phases were solved with the programs SOLVE [T. C. Terwilliger and J. Berendzen, Acta Crystallogr. D 52, 749 (1996)] and MLPHARE [Z. Otwinowsky, in Isomorphous Replacement and Anomalous Scattering, Proceedings of the CCP4 Study Weekend, W. Wolf, P. R. Evans, A. G. W. Leslie, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1991), pp. 80-86] (see Table 1). The initial MIR phases were improved by electron density averaging over the twofold noncrystallographic symmetry and solvent flattening with the program DM [K. D. Cowtan and P. Main, Acta Crystallogr. D 52, 43 (1996)]. Model building from the electron density map was done with the program O [T. A. Jones, J. Y. Zou, S. W. Cowan, M. Kjelgaard, Acta Crystallogr. A 47, 110 (1991)]. The program SigmaA [R. J. Read, ibid. 42, 140 (1986)] was used to combine phase information at initial stages of model building. Refinement was carried out with the program X-PLOR version 3.8 [A. T. Brünger, J. Kuriyan, M. Karplus, Science 235, 458 (1987)]. Noncrystallographic-symmetry constraints were used throughout the refinement. At late stages of the refinement, both grouped temperature factor refinement and a bulk solvent correction were applied. The final R factor is 21.5% over the 20.0 to 2.9 Å resolution shell (29,980 reflections), and the free R [A. T. Brünger, Nature 355, 472 (1992)] is 29.2% (3330 reflections). Bond and angle deviations are 0.009 Å and 1.57°, respectively. Structural superposition and solvent-accessible surface calculation were carried out with the program EDPDB [X. Zhang and B. W. Matthews, J. Appl. Crystallogr. 28, 624 (1995)]. Figures in this manuscript were created with MOLSCRIPT and RASTER3D [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991); E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D 50, 869 (1994)]. The coordinates of the complex have been deposited in the Brookhaven Protein Databank (1BML).
29. Diffraction data were collected on a Siemens area detector at room temperature. Molecular replacement with chymotrypsin [M. Harel, C. T. Su, F. Frolow, I. Silman, J. L. Sussman, Biochemistry 30, 5217 (1991)] as a search model established a local twofold symmetry. The MIR phases were solved with the programs SOLVE [T. C. Terwilliger and J. Berendzen, Acta Crystallogr. D 52, 749 (1996)] and MLPHARE [Z. Otwinowsky, in Isomorphous Replacement and Anomalous Scattering, Proceedings of the CCP4 Study Weekend, W. Wolf, P. R. Evans, A. G. W. Leslie, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1991), pp. 80-86] (see Table 1). The initial MIR phases were improved by electron density averaging over the twofold noncrystallographic symmetry and solvent flattening with the program DM [K. D. Cowtan and P. Main, Acta Crystallogr. D 52, 43 (1996)]. Model building from the electron density map was done with the program O [T. A. Jones, J. Y. Zou, S. W. Cowan, M. Kjelgaard, Acta Crystallogr. A 47, 110 (1991)]. The program SigmaA [R. J. Read, ibid. 42, 140 (1986)] was used to combine phase information at initial stages of model building. Refinement was carried out with the program X-PLOR version 3.8 [A. T. Brünger, J. Kuriyan, M. Karplus, Science 235, 458 (1987)]. Noncrystallographic-symmetry constraints were used throughout the refinement. At late stages of the refinement, both grouped temperature factor refinement and a bulk solvent correction were applied. The final R factor is 21.5% over the 20.0 to 2.9 Å resolution shell (29,980 reflections), and the free R [A. T. Brünger, Nature 355, 472 (1992)] is 29.2% (3330 reflections). Bond and angle deviations are 0.009 Å and 1.57°, respectively. Structural superposition and solvent-accessible surface calculation were carried out with the program EDPDB [X. Zhang and B. W. Matthews, J. Appl. Crystallogr. 28, 624 (1995)]. Figures in this manuscript were created with MOLSCRIPT and RASTER3D [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991); E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D 50, 869 (1994)]. The coordinates of the complex have been deposited in the Brookhaven Protein Databank (1BML).
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50. We thank E. Davie, B. W. Matthews, J. D. Capra, and J. Hartsuck for critical reading of this manuscript and N. Cook for technical assistance. Supported by NIH grant HL 60626, grant HR98-029 from Oklahoma Center for the Advancement of Science and Technology, and the resources of the Oklahoma Medical Research Foundation.