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unpublished results
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2-terminal methionine (C. Harrison and D. King, unpublished results). A crystal form suitable for x-ray analysis was found with the sparse matrix method [J. Jancarik and S.-H. Kim, J. Appl. Crystallogr. 24, 409 (1991)]. Crystals were grown by vapor diffusion at 8°C against 100 mM sodium acetate (pH 4.6), 200 mM ammonium acetate, and 25 to 30% PEG4000 (Fluka Chemie AG) at a final protein concentration of 15 mg/ml.
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269. Subsequent determination of the structure showed that there is poor electron density for amino acids 269 to 272, which is in part of the extended loop.
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23
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2, a value estimated from a Wilson plot of the native data between 1.9 and 2.7 Å. X-PLOR 3.1 (10) was used for all of the refinement, with the use of the force field parameters developed by R. A. Engh and R. Huber [Acta Crystallogr. A47, 392 (1991)]. As the refinement progressed through iterative cycles of simulated annealing and model building, electron density, which had not been seen previously, appeared for the solvent-exposed side chains. The extended loop was the only structural element that required some refitting in the simulated annealing omit maps.
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2, a value estimated from a Wilson plot of the native data between 1.9 and 2.7 Å. X-PLOR 3.1 (10) was used for all of the refinement, with the use of the force field parameters developed by R. A. Engh and R. Huber [Acta Crystallogr. A47, 392 (1991)]. As the refinement progressed through iterative cycles of simulated annealing and model building, electron density, which had not been seen previously, appeared for the solvent-exposed side chains. The extended loop was the only structural element that required some refitting in the simulated annealing omit maps.
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2, a value estimated from a Wilson plot of the native data between 1.9 and 2.7 Å. X-PLOR 3.1 (10) was used for all of the refinement, with the use of the force field parameters developed by R. A. Engh and R. Huber [Acta Crystallogr. A47, 392 (1991)]. As the refinement progressed through iterative cycles of simulated annealing and model building, electron density, which had not been seen previously, appeared for the solvent-exposed side chains. The extended loop was the only structural element that required some refitting in the simulated annealing omit maps.
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2, a value estimated from a Wilson plot of the native data between 1.9 and 2.7 Å. X-PLOR 3.1 (10) was used for all of the refinement, with the use of the force field parameters developed by R. A. Engh and R. Huber [Acta Crystallogr. A47, 392 (1991)]. As the refinement progressed through iterative cycles of simulated annealing and model building, electron density, which had not been seen previously, appeared for the solvent-exposed side chains. The extended loop was the only structural element that required some refitting in the simulated annealing omit maps.
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2, a value estimated from a Wilson plot of the native data between 1.9 and 2.7 Å. X-PLOR 3.1 (10) was used for all of the refinement, with the use of the force field parameters developed by R. A. Engh and R. Huber [Acta Crystallogr. A47, 392 (1991)]. As the refinement progressed through iterative cycles of simulated annealing and model building, electron density, which had not been seen previously, appeared for the solvent-exposed side chains. The extended loop was the only structural element that required some refitting in the simulated annealing omit maps.
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Both SFL-1 and SKN-7 contain the corresponding phenylalanine and leucine. SFL-1 has three amino acids between these two residues, whereas SKN-7 has four amino acids.
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We differentiate this variation from that seen in the Oct-1 POU-specific domain and HNF-1 proteins, which are members of the all α-helical class of helix-turn-helix motifs. They both have a longer turn between the two helices of the motif, but they still have the same relative positions of α2 and α3 as the canonical motif from the all aα-helical class [N. Assa-Munt, R. J. Mortishire-Smith, R. Aurora, W. Herr, P. E. Wright, Cell 73, 193 (1993); B. Leiting et al., EMBO J. 12, 1797 (1993); T. A. Ceska et al., ibid., p. 1805].
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We differentiate this variation from that seen in the Oct-1 POU-specific domain and HNF-1 proteins, which are members of the all α-helical class of helix-turn-helix motifs. They both have a longer turn between the two helices of the motif, but they still have the same relative positions of α2 and α3 as the canonical motif from the all aα-helical class [N. Assa-Munt, R. J. Mortishire-Smith, R. Aurora, W. Herr, P. E. Wright, Cell 73, 193 (1993); B. Leiting et al., EMBO J. 12, 1797 (1993); T. A. Ceska et al., ibid., p. 1805].
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We differentiate this variation from that seen in the Oct-1 POU-specific domain and HNF-1 proteins, which are members of the all α-helical class of helix-turn-helix motifs. They both have a longer turn between the two helices of the motif, but they still have the same relative positions of α2 and α3 as the canonical motif from the all aα-helical class [N. Assa-Munt, R. J. Mortishire-Smith, R. Aurora, W. Herr, P. E. Wright, Cell 73, 193 (1993); B. Leiting et al., EMBO J. 12, 1797 (1993); T. A. Ceska et al., ibid., p. 1805].
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note
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We thank A. de Vos for help, advice, and time on the FAST at Genentech; D. King for advice on purification and for electrospray-ionization mass spectrometry; R. Standeart for advice on selenomethionine incorporation; R. Stevens, J. Somoza, and T. Earnest for help and advice on crystallography; D. Heinz and S. Burley for sending us preprints of their manuscripts; and all of the members of the Nelson laboratory. This work was partially supported by NIH grant GM44086 (H.C.M.N.) and an award from the Pew Scholars Program in Biomedical Sciences (H.C.M.N.). Instrumentation was funded in part by funds provided from the Lucille P. Markey Charitable Trust through the Berkeley campus Program in Biomolecular Structure and Design. C.J.H. was supported in part by an NSF Graduate Research Fellowship and by U.S. Public Health Service predoctoral training grant GM08295. A.A.B. was supported by the director, Office of Energy Research, Office of Health Effects, of the U.S. Department of Energy under contract DE-AC03-76SF00098.
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