摘要:

The crystal structure of the ternary complex of horse liver alcohol dehydrogenase (LADH) with the coenzyme NADH and inhibitor dimethyl sulfoxide (DMSO) has been refined by simulated annealing with molecular dynamics and restrained positional refinement using the programX‐PLOR. The two subunits of the enzyme were refined independently. The space group wasP1 with cell dimensionsa= 51.8,b= 44.5,c= 94.6 Å, α = 104.8, β = 102.3 and γ = 70.6°. The resulting crystallographicRfactor is 17.3% for 62 440 unique reflections in the resolution range 10.0–1.8 Å. A total of 472 ordered solvent molecules were localized in the structure. An analysis of secondary‐structure elements, solvent content and NADH bin

ISSN:1399-0047    

DOI:10.1107/S0907444994005263

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

To assess the accuracy of refined structures, a comparison was made using independently determined structures of the same protein in the same crystal form. The models were re‐refined against a common data set to minimize the effects of different data and different refinement protocols. The process did not converge to a single model. Rather the structures differed from each other by 0.84 Å which was roughly three times that predicted by a Luzzati analysis [Luzzati (1952).Acta Cryst.5, 802810]. The individual structures are equally valid and at least partially independent as evidenced by a reduction of theRfactor by 0.013 when a simple linear combination is used. Only 29 solvent molecules were common to all four mo

ISSN:1399-0047    

DOI:10.1107/S0907444994002659

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

Three crystal forms of the sweet‐tasting protein thaumatin from the African berryThaumatococcus danielliihave been grown. These include two naturally occurring isoforms,AandB, that differ by a single amino acid, and a recombinant form of isoformBexpressed in yeast. The crystals are of space groupsC2 witha= 117.7,b= 44.9,c= 38.0 Å, and β = 94.0°,P212121witha= 44.3,b= 63.7 andc= 72.7 Å, and a tetragonal formP41212 witha=b= 58.6 andc= 151.8 Å. The structures of all three crystals have been solved by molecular replacement and subsequently refined toRfactors of 0.184 for the monoclinic at 2.6 Å, 0.165 for the orthorhombic at 1.75 Å, and 0.181 for the tetragonal, also at 1.75 Å resolution. No solvent was included in the monoclinic crystal while 123 and 105 water molecules were included in the higher resolution orthorhombic and tetragonal structures, respectively. A bound tartrate molecule was also clearly visible in the tetragonal structure. The r.m.s. deviations between molecular structures in the three crystals range from 0.6 to 0.7 Å for Cα atoms, and 1.1 to 1.3 Å for all atoms. This is comparable to the r.m.s. deviation between the three structures and the starting model. Nevertheless, several peptide loops show particularly large varia

ISSN:1399-0047    

DOI:10.1107/S0907444994005512

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

The crystal structure of glutaminase–asparaginase fromAcinetobacter glutaminasificanshas been reinterpreted and refined to anRfactor of 0.171 at 2.9 Å resolution, using the same X‐ray diffraction data that were used to build a preliminary model of this enzyme [Ammon, Weber, Wlodawer, Harrison, Gilliland, Murphy, Sjölin&Roberts (1988).J. Biol. Chem.263, 150–156]. The current model, which does not include solvent, is based in part on the related structure ofEscherichia coliasparaginase and is significantly different from the structure of the enzyme fromA. glutaminasificansdescribed previously. The reason for the discrepancies has been traced to insufficient phasing power of the original heavy‐atom derivative data, which could not be compensated for fully by electron‐density modification techniques. The corrected structure ofA. glutaminasificansglutaminase–asparaginase is presented and compared with the preliminary model and with the structure ofE.

ISSN:1399-0047    

DOI:10.1107/S0907444994003446

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

The direct methods programSAYTANwas applied to simulated data at various resolutions from three oligonucleotides. Success in solving the structures was found to depend more upon the resolution of the data than upon errors in the data or the complexity of the structure. Collecting the data at a reduced temperature has little effect, unless it alters the mosaicity of the crystal or changes the resolution of the data. The presence of a heavy atom dramatically improved the phase refinement, particularly at low resolution.

ISSN:1399-0047    

DOI:10.1107/S0907444994005615

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

In recent years it has been shown that direct methods are capable of solving the structures of small proteins. Mukherjee&Woolfson [Acta Cryst. (1993), D49, 912] have shown that useful phase sets can be produced even at 3 Å resolution but that the standard figures of merit could not distinguish the better phase sets from others. They found modified forms of the standard figures of merit that could pick out better phase sets for 2 Å resolution or higher. Gilmore, Henderson&Bricogne [Acta Cryst. (1991), A47, 842846] have shown that evaluation of the log‐likelihood gain, coming from entropy‐maximization procedures, is also very successful in picking out good protein phases sets. A new figure of merit is described, based on the expected charactistics of an electron‐density map for a protein, and comparisons are made with the other figures of merit ment

ISSN:1399-0047    

DOI:10.1107/S0907444994006323

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

The three‐dimensional structure of the complex between methyl α‐d‐mannopyranoside and concanavalin A has been refined at 2.0 Å resolution. Diffraction data were recorded from a single crystal (space groupP212121,a= 123.7,b= 128.6,c= 67.2 Å) using synchrotron radiation at a wavelength of 1.488 Å. The final model has good geometry and anRfactor of 19.9% for 58 871 reflections (82% complete), within the resolution limits of 8 to 2 Å, withF>1.0σ(F). The asymmetric unit contains four protein subunits arranged as a dimer of dimers with approximate 222 point symmetry. Each monomer binds one saccharide molecule. Each sugar is bound to the protein by hydrogen bonds and van der Waals contacts. Although the four subunits are not crystallographically equivalent, the protein–saccharide interactions are nearly identical in each of the four binding sites. The differences that do occur between the four sites are in the structure of the water network which surrounds each saccharide; these networks are involved in crystal packing. The structure of the complex is compared with a refined saccharide‐free concanavalin A structure. The saccharide‐free structure is composed of crystallographically identical subunits, again assembled as a dimer of dimers, but with exact 222 symmetry. In the saccharide complex the tetramer association is different in that the monomers tend to separate resulting in fewer intersubunit interactions. The average temperature factor of the mannoside complex is considerably higher than that of the saccharide‐free protein. The binding site in the saccharide‐free structure is occupied by three ordered water molecules and the side chain of Asp71 from a neighbouring molecule in the crystal. These occupy positions similar to those of the four saccharide hydroxyls which are hydrogen bonded to the site. Superposition of the saccharide‐binding site from each structure shows that the major changes on binding involve expulsion of these ordered solvents and the reorientation of the side chain of Tyrl00. Overall the surface accessibility of the saccharide decreases from 370 to 100 Å2when it binds to the protein. This work builds upon the earlier studies of Derewendaet al. [Derewenda, Yariv, Helliwell, Kalb (Gilboa), Dodson, Papiz, Wan&Campbell (1989).EMBO J.8, 2198–2193] at 2.9 Å resolution, which was the first detaile

ISSN:1399-0047    

DOI:10.1107/S0907444994005287

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

The crystal structures of porcine and human aldehyde reductase, an enzyme implicated in complications of diabetes, have been determined by X‐ray diffraction methods. The crystallographicRfactor for the refined porcine aldehyde reductase model is 0.19 at 2.8 Å resolution. There are two molecules in the asymmetric unit related by a local non‐crystallographic twofold axis. The human aldehyde reductase model has been refined to anRfactor of 0.21 at 2.48 Å resolution. The amino‐acid sequence of porcine aldehyde reductase revealed a remarkable homology with human aldehyde reductase. The coenzyme‐binding site residues are conserved and adopt similar conformations in human and porcine aldehyde reductase apo‐enzymes. The tertiary structures of aldhyde reductase and aldose reductase are similar and consist of a β/α‐barrel, with the coenzyme‐binding site located at the carboxy‐terminus end of the strands of the barrel. The crystal structure of porcine and human aldehyde reductase should allowin vitromutagenesis to elucidate the mechanism of action for this enzyme and facilitate the effective design

ISSN:1399-0047    

DOI:10.1107/S0907444994005275

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

Raster3DVersion 2.0 is a program suite for the production of photorealistic molecular graphics images. The code is hardware independent, and is particularly suited for use in producing large raster images of macromolecules for output to a film recorder or high‐quality color printer. TheRaster3Dsuite contains programs for composing illustrations of space‐filling models, ball‐and‐stick models and ribbon‐and‐cylinder representations. It may also be used to render figures composed using other graphics tools, notably the widely used programMolscript[Kraulis (1991).J. Appl. Cryst.

ISSN:1399-0047    

DOI:10.1107/S0907444994006396

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

This paper describes the study of the effects of radiation damage on the quality of data collected from a protein crystal at 100 K. It is shown that radiation damage causes measurable effects in the diffraction pattern. This implies that, even at liquid nitrogen temperatures, there is a limit to the size of a crystal from which a complete data set can be collecte

ISSN:1399-0047    

DOI:10.1107/S0907444994006311

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY