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  • 1
    Electronic Resource
    Electronic Resource
    Structure of copper- and oxalate-substituted human lactoferrin at 2.0 Å resolution (1994)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 50 (1994), S. 302-316 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The three-dimensional structure of human dicupric monooxalate lactoferrin, Cu2oxLf, has been determined to 2.0 Å resolution, using X-ray diffraction data collected by diffractometry to 2.5 Å resolution, and oscillation photography on a synchrotron source to 2.0 Å resolution. Difference electron-density maps calculated between Cu2oxLf and both dicupric lactoferrin, Cu2Lf, and diferric lactoferrin, Fe2Lf, showed that the oxalate had replaced a carbonate in the C-terminal binding site, and that, relative to Cu2Lf, there were no significant differences in the N-terminal site. The structure was then refined crystallographically by restrained least-squares methods. The final model, in which the r.m.s. deviation in bond distances is 0.017 Å, contains 5314 protein atoms (691 residues), two Cu2+ ions, one bicarbonate ion, one oxalate ion, 325 solvent molecules and one sugar residue. The crystallographic R factor of 0.193 is for 46 134 reflections in the range 8.0 to 2.0 Å resolution. The oxalate ion is coordinated to copper in a 1,2-bidentate fashion, and the added bulk of the anion results in the rearrangement of the side chains of nearby arginine and tyrosine residues. No other major alterations in the molecule can be observed, the overall protein structure being the same as that for Cu2Lf and Fe2Lf.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994000491
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  • 2
    Electronic Resource
    Electronic Resource
    Search designs for protein crystallization based on orthogonal arrays (1994)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 50 (1994), S. 429-440 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In protein crystallography, the initial experimental problem is the identification of physical and chemical conditions that will support nucleation and crystal growth. Ideally, experiments to search for such conditions would be based on a full-factorial structure, with variation in the temperature and solution composition. However, consideration of even a moderate number of possibilities for the composition of the system will result in factorial experiments which may be prohibitively large. In this paper it is proposed that search experiments for protein crystallization might be based on orthogonal arrays. These are subsets of full-factorial experiments which possess a great deal of symmetry, such that a uniform distribution of points throughout the experimental region is preserved. Such experiments have reasonable size, explore the proposed experimental region in a systematic fashion, and form a logical basis for a sequential approach to the search for crystallization conditions. Examples of such initial search experiments are given, and their application to some recent protein crystallization problems in this laboratory is described briefly. The relationship of this approach to other protein crystallization search procedures is also discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993014374
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  • 3
    Electronic Resource
    Electronic Resource
    Enzymatic deglycosylation as a tool for crystallization of mamalian binding proteins (1994)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 50 (1994), S. 380-384 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Enzymatic deglycosylation has been used in attempts to crystallize several glycoproteins with the aim of overcoming the problems resulting from heterogeneity and flexibility of the attached glycan chains. An endoglycosidase preparation from Flavobacterium meningosepticum, comprising the enzymes endo F and PNGase-F, was used in experiments on the mammalian binding proteins lactoferrin and haemopexin. Significant differences were found in the susceptibility of different proteins to deglycosylation. For human lactoferrin (Lf) and its recombinant N-terminal half-molecule (LfN), deglycosylation was rapid and complete, and was essential for obtaining high-quality crystals of both apo-Lf and LfN; for bovine Lf, however, complete deglycosylation did not occur. Similarly, for rabbit haemopexin the carbohydrate chain on the C-terminal domain was easily removed, but the three chains on the N-terminal domain proved more resistant and their removal led to some fragmentation of the protein. Nevertheless, this approach provided the only means of crystallizing the C-terminal domain and is likely to be useful for other glycoproteins.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993013435
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  • 4
    Electronic Resource
    Electronic Resource
    PRISM: topologically constrained phased refinement for macromolecular crystallography (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 429-439 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: We describe the further development of phase refinement by iterative skeletonization (PRISM), a recently introduced phase-refinement strategy [Wilson & Agard (1993). Acta Cryst. A49, 97–104] which makes use of the information that proteins consist of connected linear chains of atoms. An initial electron-density map is generated with inaccurate phases derived from a partial structure or from isomorphous replacement. A linear connected skeleton is then constructed from the map using a modified version of Greer's algorithm [Greer (1985). Methods Enzymol. 115, 206–226] and a new map is created from the skeleton. This `skeletonized' map is Fourier transformed to obtained new phases, which are combined with any starting-phase information and the experimental structure-factor amplitudes to produce a new map. The procedure is iterated until convergence is reached. In this paper significant improvements to the method are described as is a challenging molecular-replacement test case in which initial phases are calculated from a model containing only one third of the atoms of the intact protein. Application of the skeletonization procedure yields an easily interpretable map. In contrast, application of solvent flattening does not significantly improve the starting map. The iterative skeletonization procedure performs well in the presence of random noise and missing data, but requires Fourier data to at least 3.0 Å. The constraints of linearity and connectedness prove strong enough to restore not only missing phase information, but also missing amplitudes. This enables the use of a powerful statistical test, analogous to the `free R factor' of conventional refinement [Brünger (1992). Nature (London), 355, 472–474], for optimizing the performance of the skeletonization procedure. In the accompanying paper, we describe the application of the method to the solution of the structure of the protease inhibitor ecotin bound to trypsin and to a single isomorphous replacement problem.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993004032
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  • 5
    Electronic Resource
    Electronic Resource
    PRISM: application to the solution of two protein structures (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 440-448 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The previous paper described a phase-refinement strategy for protein crystallography which exploited the information that proteins consist of connected linear chains of atoms. Here the method is applied to a molecular-replacement problem, the structure of the protease inhibitor ecotin bound to trypsin, and a single isomorphous replacement problem, the structure of the N-terminal domain of apolipoprotein E. The starting phases for the ecotin-trypsin complex were based on a partial model (trypsin) containing 61% of the atoms in the complex. Iterative skeletonization gave better results than either solvent flattening or twofold non-crystallographic symmetry averaging as measured by the reduction in the free R factor [Brünger (1992). Nature (London), 355, 472–474]. Protection of the trypsin density during the course of the refinement greatly improved the performance of both skeletonizing and solvent flattening. In the case of apolipoprotein E, previous attempts using solvent flattening had failed to improve the SIR phases to the point of obtaining an interpretable map. The combination of iterative skeletonization and solvent flattening decreased the phase error with respect to the final refined structure, significantly more than solvent flattening alone. The final maps generated by the skeletonization procedure for both the ecotin–trypsin complex and apolipoprotein E were readily interpretable.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993004020
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  • 6
    Electronic Resource
    Electronic Resource
    Metal substitution in a blue-copper protein: the crystal structure of cadmium-azurin at 1.8 Å resolution (1994)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 50 (1994), S. 263-270 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of cadmium-substituted azurin have been prepared by diffusing CdII into crystals of apo-azurin grown previously and their structure has been determined at high resolution by X-ray crystallography. Data to 1.8 Å resolution were collected by Weissenberg photography (with image plates) using synchrotron radiation. These data were combined with a 2.2 Å diffractometer data set to give 90% coverage to 1.8 Å. An initial model was derived from the isomorphous CuII-azurin structure, and the cadmium and ligand positions added from `omit' maps. Refinement was by restrained least squares (program PROLSQ), to a final R value of 0.168 for all data in the range 10.0–1.8 Å (23 349 reflections). The final model of 1954 protein atoms, two CdII ions (occupancy 0.75), four SO{_4^{2-}} ions and 239 water molecules has r.m.s. deviations of 0.015, 0.045 and 0.013 Å from standard bond lengths, angle distances and planar groups. The protein structure is essentially the same as that of CuII-azurin, with an r.m.s. deviation of 0.18 Å for 97% of main-chain atoms after superposition of the two structures. The Cd atom is within 0.2 Å of the equivalent copper position, displaced slightly away from the axial Met ligand towards the carbonyl O atom of Gly45. The latter has also moved slightly towards the metal, by a rotation of the peptide unit, to give a Cd—O bond of 2.76 Å. The Cd—S(Cys) bond is lengthened to 2.39 Å. The coordination geometry is slightly more tetrahedral than for CuII, and the cadmium–oxygen interaction is consistent with the presence of an oxygen ligand in the coordination sphere of stellacyanin.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993014398
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  • 7
    Electronic Resource
    Electronic Resource
    Uniqueness and the ab initio phase problem in macromolecular crystallography (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 186-192 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystallographic phase problem is indeterminate in the absence of additional chemical information. A successful ab initio approach to the macromolecular phase problem must employ sufficient chemical constraints to limit the solutions to a manageably small number. Here we show that commonly employed chemical constraints – positivity, atomicity and a solvent boundary – leave the phase problem greatly underdetermined for Fourier data sets of moderate (2.5–3.0 Å) resolution. Entropy maximization is also beset by multiple false solutions: electron-density maps are readily generated which satisfy the same Fourier amplitude constraints but have higher entropies than the true solution. We conclude that a successful ab initio approach must make use of high-resolution Fourier data and/or stronger chemical constraints. One such constraint is the connectivity of the macromolecule. We describe a rapid algorithm for measuring the connectivity of a map, and show its utility in reducing the multiplicity of solutions to the phase problem.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444992008801
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  • 8
    Electronic Resource
    Electronic Resource
    Structure of apo-azurin from Alcaligenes denitrificans at 1.8 Å resolution (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 331-343 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of apo-azurin from Alcaligenes denitrificans has been determined at high resolution by X-ray crystallography. Two separate structure analyses have been carried out, (i) on crystals obtained from solutions of apo-azurin and (ii) on crystals obtained by removal of copper from previously formed crystals of holo-azurin. Data to 1.8 Å resolution were collected from the apo-azurin crystals, by Weissenberg photography (with image plates) using synchrotron radiation and by diffractometry, and the structure was refined by restrained least-squares methods to a final R value of 0.160 for all data in the range 10.0–1.8 Å. The final model of 1954 protein atoms, 246 water molecules (66 half-weighted), four SO42− ions, and two low-occupancy (0.13 and 0.15) Cu atoms has r.m.s. deviations of 0.012, 0.045 and 0.013 Å from standard bond lengths, angle distances and planar groups. For copper-removed azurin, data to 2.2 Å were collected by diffractometry and the structure refined by restrained least squares to a final R value of 0.158 for all data in the range 10.0–2.2 Å. The final model of 1954 protein atoms, 264 water molecules, two SO42− ions, two low occupancy (0.18 and 0.22) metal atoms and one unidentified atom (modelled as S) has r.m.s. deviations of 0.013, 0.047 and 0.012 Å from standard bond lengths, angle distances and planar groups. The two structures are essentially identical to each other and show no significant differences from the oxidized and reduced holo-azurin structures. The ligand side chains move slightly closer together following the removal of copper, with the radius of the cavity between the three strongly binding ligands, His 46, His 117 and Cys 112, shrinking from 1.31 Å in reduced azurin to 1.24 Å in oxidized azurin and 1.16 Å in apo-azurin. There is a suggestion of increased flexibility in one of the copper-binding loops but the structure supports the view that the copper site found in holo-azurin is a stable structure, defined by the constraints of the polypeptide structure even in the absence of a bound metal ion.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444992013544
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  • 9
    Electronic Resource
    Electronic Resource
    Copper, John F.; Lee, Ta-ling: Tiananmen Aftermath: Human Rights in the People's Republic of China, 1990 : Baltimore, University of Maryland, 1992 (1993)
    Cambridge : Cambridge University Press
    The @China quarterly 135 (1993), S. 583-584 
    Details
    ISSN: 0305-7410
    Source: Cambridge Journals Digital Archives
    Topics: Linguistics and Literary Studies , History , Political Science , Sociology , Economics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1017/S0305741000014004
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  • 10
    Electronic Resource
    Electronic Resource
    Social Change in Hong Kong: Hong Kong Man in Search of Majority (1993)
    Cambridge : Cambridge University Press
    The @China quarterly 136 (1993), S. 864-877 
    Details
    ISSN: 0305-7410
    Source: Cambridge Journals Digital Archives
    Topics: Linguistics and Literary Studies , History , Political Science , Sociology , Economics
    Notes: In 1983 when The China Quarterly published a special issue on Hong Kong, I attempted to synthesize the history of its urban social life, coining the term “Hong Kong Man” to describe what I considered to be the emergence of an identifiable unique social animal. Hong Kong Man, I suggested, was neither Chinese nor British. I characterized him as quick-thinking, flexible, tough for survival, excitement-craving, sophisticated in material tastes, and self-made in a strenuously competitive world. He operated in the context of a most uncertain future, control over which was in the hands of others, and for this as well as for historical reasons he lived “life in the short term”.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1017/S0305741000032367
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