摘要:

The speed of electron‐density fitting during X‐ray structure solution and refinement, and the quality of the protein model resulting, can both be enhanced by the use of databases of main‐ and side‐chain conformations. Three structures are compared in this report, one refined at high resolution (1.7 Å), and two at lower resolutions using either the database method (2.4 Å resolution) or more traditional empirical electron‐density fitting (1.9 Å resolution). An analysis of peptide orientation was used as an aid in finding unusual portions of main‐chain structure. The fit of side chains to known rotamer conformations was used to help determine the accuracy of these atomic positions. In addition, the use of an objective measure of the fit of structures to electron‐density maps was evaluated, both alone and in combination with side‐chain co

ISSN:1399-0047    

DOI:10.1107/S0907444993011321

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

A monoclinic crystal of hen egg lysozyme (HEL, E.C. 3.2.1.17) was obtained at 313 K from a 10%(w/v) NaCl solution at pH 7.6 containing 5%(v/v) 1‐propanol. Cell dimensions werea= 27.23,b= 63.66,c= 59.12 A and β = 92.9°, and the space group wasP21. The unit cell contains four molecules (Vm= 1.79 Å3 Da−1). The structure was solved by the isomorphous replacement method with anomalous scattering followed by phase improvement by the solvent‐flattening method. The refinement of the structure was carried out by the simulated‐annealing method. The conventionalRvalue was 0.187 for 18 260 reflections [|Fo|>3σ(F)] in the resolution range 10–1.72 Å. The r.m.s. deviations from the ideal bond distances and angles were 0.015 Å and 3.0°, respectively. The two molecules in the asymmetric unit are related by a translation of half a lattice unit along theaandcaxes. The r.m.s. difference of equivalent Cαatoms between the two molecules was 0.64 Å and the largest difference was 3.57 Å for Gly71. A significant structural change was observed in the regions of residues 45–50, 65–73 and 100–104. The residues 45–50, which connect two β‐strands, are shifted parallel to the β‐sheet plane between the two molecules. The residues 100–104 belong to the substrate‐binding site (subsiteA) and the high flexibility of this region may be responsible for the bind

ISSN:1399-0047    

DOI:10.1107/S0907444993013290

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

The crystal structure is described of ribulose 1,5‐bisphosphate carboxylase/oxygenase in a new crystal form. This new form (form V) was obtained from a previously known crystal form (form III) through a solid‐state phase transition. The solid‐state phase transition was brought about by transferring the crystal from a high‐salt low‐pH mother liquor to a low‐salt high‐pH synthetic mother liquor. The interplay of electrostatic repulsion and osmotic pressure induced a unit‐cell shrinkage of 24 Å along thecaxis and expansion of 4 Å along theaandbaxes. The space group also changed fromI422 toI4. The new crystal form was shown to be more resistant to X‐ray radiation damage, which suggests the effect of crystal stabilization by non‐penetrating molecules. The structure of ribulose 1,5‐bisphosphate carboxylase/oxygenase in the new crystal form is compared with t

ISSN:1399-0047    

DOI:10.1107/S090744499301306X

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

Crystals of cadmium‐substituted azurin have been prepared by diffusing CdIIinto 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 (programPROLSQ), to a finalRvalue 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 CdIIions (occupancy 0.75), four SO 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 l

ISSN:1399-0047    

DOI:10.1107/S0907444993014398

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

An automatic molecular‐replacement procedure has been applied to solve the crystal structure of cytochromec2fromRhodopseudomonas viridis. The structure was solved on the basis of the structure of tuna cytochromecas a search model using an automatic processing program system,AUTOMR. The refinements by molecular dynamics and restrained least‐squares methods result in a current crystallographicRfactor of 0.219 for diffraction data at 3 Å reso

ISSN:1399-0047    

DOI:10.1107/S0907444993013952

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

The development of high‐intensity X‐ray sources and the use of insertion devices will make it possible to collect data routinely from protein crystals at very short wavelengths (λ≤ 0.5 Å). Possible benefits of using shorter wavelengths can be inferred from the improvement in the quality of the data when using a wavelength λ≃ 0.9 Å instead of one close to the Cu Kα emission edge. In addition to fewer absorption errors, two factors might contribute to this improvement. These are an increase in the lifetime of the protein crystal and a better signal‐to‐background ratio. In this paper we address the second of these. In order to compare the quality of the data and the relative background level in the diffraction patterns at different wavelengths two data sets have been collected at λ = 0.92 and 0.55 Å. The results obtained from data processing and careful measurement of the background in the raw images suggest that, in the absence of absorption errors and radiation damage, data collection at very short wavelengths does not provide higher quality data. There is no improvement in the signal‐to‐background rati

ISSN:1399-0047    

DOI:10.1107/S0907444993013101

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

The crystal structure of metmyoglobin from yellowfin tuna (Thunnus albacares) has been determined by molecular replacement methods and refined to a conventionalRfactor of 0.177 for all observed reflections in the range of 6.0–1.70 Å resolution. Like other myoglobins for which a high‐resolution structure is available, the polypeptide chain is organized into several helices that cooperate to form a hydrophobic pocket into which the heme prosthetic group is non‐covalently bound; however, theDhelix observed in other myoglobins is absent in myoglobin from yellowfin tuna and has been replaced with a random coil. As well, theAhelix has a pronounced kink due to the presence of Pro16. The differences in structure between this and sperm whale myoglobin can be correlated with their reported dioxygen affinity and dissociation. The structure is in agreement with reported fluorescence data which show an increased Trp14⋯heme distance in yellowfin tuna compared to sperm whale

ISSN:1399-0047    

DOI:10.1107/S0907444993014271

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

High‐resolution single crystals of a catalytic RNA molecule derived from the sequence of the satellite RNA of tobacco ringspot virus have been obtained. The unit‐cell volumes of the RNA crystals vary depending on the crystallization conditions and temperature. The best crystal form, when flash frozen, has space groupP1 with unit‐cell dimensionsa= 53.08,b= 71.81,c= 28.03 Å, α = 98.43, β = 104.32 and γ = 74.54°. This form diffracts to a resolution of 2.4 Å. A heavy‐atom derivative sear

ISSN:1399-0047    

DOI:10.1107/S0907444993013071

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

The automated microbatch technique developed at Imperial College has been used to establish a phase diagram for crystallization. The concentrations of the protein (carboxypeptidase G2) and precipitant (PEG 4000) were varied, while pH and temperature were kept constant. The diagram consists of an undersaturation and a supersaturation zone, the latter being subdivided into the metastable, nucleation and precipitation zones. In the metastable zone, crystals may grow but nucleation of crystals does not occur. It is the best zone for growth of X‐ray diffraction quality crystals because of the slower growth rate and the avoidance of uncontrolled nucleation, which uses up protein in the formation of tiny crystals. Nevertheless, in practice, it is rarely well defined or used because nuclei must be introduced artificially into the system. The new method used here consists of setting crystallization droplets at nucleation conditions and later diluting them to conditions where nucleation has not been observed. Single diffracting crystals of typical dimensions 0.3 × 0.3 × 0.2 mm were routinely obtained in the metastable zone, equivalent to the best (very rarely) obtained crystals in the nucleation

ISSN:1399-0047    

DOI:10.1107/S0907444993013186

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

Two hexagonal crystal forms of tetrameric human methylamine‐treated α2‐macroglobulin have been grown by vapour diffusion. One of the crystal forms diffracts X‐rays beyond 9 Å resolution. The space group of this form isP6(2)22 orP6(4)22 witha=b= 327,c= 219 Å and with one dimer of α2‐macroglobulin in the asymmetric unit. Several data sets have been collected by the use of synchrotron radiation at cryogenic temperature. A native data set extending to 10 Å resolution has been obtained. The mergingRfactor of t

ISSN:1399-0047    

DOI:10.1107/S0907444993013125

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY