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6
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0032562571
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O. Nureki et al., Science 280, 578 (1998).
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Science
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Nureki, O.1
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11
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0344928885
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note
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To position an aminoacyl-adenylate analogue (QSI) from the glutaminyl-tRNA ternary complex (10) into the IleRS structure, we used the program O to superimpose α-carbon atoms from the Rossmann folds of the GlnRS and IleRS complexes; α-carbons that superimposed with a difference of less than 2.5 Å were used.
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13
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0016044321
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F. Suddath et al., Nature 248, 20 (1974).
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(1974)
Nature
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Suddath, F.1
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14
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0024392753
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M. A. Rould, J. J. Perona, D. Söll, Science 246, 1135 (1989); J. J. Perona, M. A. Rould, T. A. Steitz, Biochemistry 32, 8758 (1993).
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Rould, M.A.1
Perona, J.J.2
Söll, D.3
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15
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0027165755
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M. A. Rould, J. J. Perona, D. Söll, Science 246, 1135 (1989); J. J. Perona, M. A. Rould, T. A. Steitz, Biochemistry 32, 8758 (1993).
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Biochemistry
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Perona, J.J.1
Rould, M.A.2
Steitz, T.A.3
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16
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0344497782
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note
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Ile, we superimposed the phosphate backbone of nudeotides 72 to 74 on A-form RNA, which was then used to extend the 3′ tail by 2 nucleotides.
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18
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0000893081
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P. S. Freemont, J. M. Friedman, L. S. Beese, Proc. Natl. Acad. Sci. U.S.A. 85, 8924 (1988); L. S. Beese and T. A. Steitz, EMBO J. 10, 25 (1991); C. M. Joyce and T. A. Steitz, Annu. Rev. Biochem. 63, 777 (1994).
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(1988)
Proc. Natl. Acad. Sci. U.S.A.
, vol.85
, pp. 8924
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Freemont, P.S.1
Friedman, J.M.2
Beese, L.S.3
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19
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0026019625
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P. S. Freemont, J. M. Friedman, L. S. Beese, Proc. Natl. Acad. Sci. U.S.A. 85, 8924 (1988); L. S. Beese and T. A. Steitz, EMBO J. 10, 25 (1991); C. M. Joyce and T. A. Steitz, Annu. Rev. Biochem. 63, 777 (1994).
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(1991)
EMBO J.
, vol.10
, pp. 25
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Beese, L.S.1
Steitz, T.A.2
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20
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0028206048
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P. S. Freemont, J. M. Friedman, L. S. Beese, Proc. Natl. Acad. Sci. U.S.A. 85, 8924 (1988); L. S. Beese and T. A. Steitz, EMBO J. 10, 25 (1991); C. M. Joyce and T. A. Steitz, Annu. Rev. Biochem. 63, 777 (1994).
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Annu. Rev. Biochem.
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Joyce, C.M.1
Steitz, T.A.2
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22
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0344497781
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unpublished data
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J. Wang, unpublished data.
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Wang, J.1
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23
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0028103275
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CCP4: Collaborative Computational Project No. 4, Acta Crystallogr. D 50, 760 (1994).
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(1994)
Acta Crystallogr. D
, vol.50
, pp. 760
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28
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0344497780
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note
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2, and 0.1% β-octyl glucopyranoside. The drops were streak-seeded without prior equilibration and then equilibrated at 20°C by the hanging-drop method. Crystals were frozen by replacing the mother liquor with a cryoprotectant containing the well solution with the addition of PEG 6K to a final concentration of 20% (w/v) and ethylene glycol to a final concentration of 15% (v/v) and then flash-freezing in liquid propane.
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30
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0344066613
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note
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Derivatives were phased in MLPhare with CCP4 by an innovative method called permuting the native/derivative (19). In this procedure, data collected at each of the MAD wavelengths were considered the *native" in four parallel MIR refinements, and then phases from all four refinements were combined by their Hendrickson-Lattmann coefficients in SigmaA (20). We measured phase improvement by the objective criterion of monitoring the height of a difference Fourier peak of an independent derivative for which there was a clear difference Patterson peak. Using the selenium derived phases, we identified additional sites in other derivatives. The MAD and MIR phase sets from all derivatives were combined by using SigmaA weighting and the resultant map was modified in Solomon (21). In a second round, the heavy atom parameters were independently refined by using density-modified external phases (22) and all phase sets were combined again. In the large cell, we traced the course of the backbone of the entire protein by using experimental maps with the exception of a region between residues 205 and 390 in the editing (CP1) domain and the last 4 nucleotides of the tRNA. In the small cell, the entire protein is ordered with the exception of the COOH-terminal, Zn-binding domain, a region between residues 205 and 390 in the editing domain, and the last 2 nucleotides of the tRNA (Fig. 1B). Improvement in the phases was monitored by an increase in the real space correlation coefficient in O (23). After this manuscript was submitted, the coordinates of T. thermophilus IleRS (6) became available and we used them to improve and extend our incomplete model of the editing domain.
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32
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0039202969
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Atlanta, GA, abstract TRN07
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A. M. Friedman, T. O. Fischmann, Y. Shamoo, American Crystallographic Association Annual Meeting, Atlanta, GA, abstract TRN07 (1994).
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(1994)
American Crystallographic Association Annual Meeting
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Friedman, A.M.1
Fischmann, T.O.2
Shamoo, Y.3
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34
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0345360267
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note
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Ile gene used for tRNA transcription; T. Terwilliger, R. Sweet, L. Berman, and C. Ogata for access to beamlines at Brookhaven National Laboratory, and D. Thiel for Beamlines at Cornell High Energy Synchrotron Source. We thank C. Cornell, S. Kamtekar, G. Cheetham, C. Brautigam, J. Ippolito, P. Klosterman, N. Ban, S. Szep, V. Korada, and J. Pata for help collecting data. Coordinates of the IleRS:tRNA Mupirocin complex and the structure factor amplitudes have been deposited in the Protein Data Bank (accession codes PDB 1QU2 and PDB 1QU3) and in Research Collaborating for Structural Bioinformatics at the University of New Jersey, Rutgers (RCSB009293).
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