Three-dimensional crystal structures of Escherichia coli met repressor with and without corepressor

Nature ◽  
1989 ◽  
Vol 341 (6244) ◽  
pp. 705-710 ◽  
Author(s):  
John B. Rafferty ◽  
William S. Somers ◽  
Isabella Saint-Girons ◽  
Simon E. V. Phillips
Keyword(s):  
Escherichia Coli ◽  
Crystal Structures ◽  
Three Dimensional ◽  
Dimensional Crystal

Structures of the ZrZn22 family: suprapolyhedral nanoclusters, methods of self-assembly and superstructural ordering

2009 ◽  
Vol 65 (3) ◽  
pp. 300-307 ◽  
Author(s):  
G. D. Ilyushin ◽  
V. A. Blatov
Keyword(s):  
Crystal Structures ◽  
Self Assembly ◽  
Topological Analysis ◽  
Three Dimensional ◽  
Topological Type ◽  
Point Symmetry ◽  
Two Dimensional ◽  
The Matrix ◽  
Nanocluster Precursor ◽  
Dimensional Crystal

A combinatorial topological analysis is carried out by means of the program package TOPOS4.0 [Blatov (2006), IUCr Comput. Commun. Newsl. 7, 4–38] and the matrix self-assembly is modeled for crystal structures of the ZrZn22 family (space group Fd\bar 3m, Pearson code cF184), including the compounds with superstructural ordering. A number of strict rules are proposed to model the crystal structures of intermetallics as a network of cluster precursors. According to these rules the self-assembly of the ZrZn22-like structures was considered within the hierarchical scheme: primary polyhedral cluster → zero-dimensional nanocluster precursor → one-dimensional primary chain → two-dimensional microlayer → three-dimensional microframework (three-dimensional supraprecursor). The suprapolyhedral cluster precursor AB 2 X 37 of diameter ∼ 12 Å and volume ∼ 350 Å3 consists of three polyhedra (one AX 16 of the \bar 43m point symmetry and two regular icosahedra BX 12 of the \bar 3m point symmetry); the packing of the clusters determines the translations in the resulting crystal structure. A novel topological type of the two-dimensional crystal-forming 4,4-coordinated binodal net AB 2, with the Schläfli symbols 3636 and 3366 for nodes A and B, is discovered. It is shown that the ZrZn22 superstructures are formed by substituting some atoms in the cluster precursors. Computer analysis of the CRYSTMET and ICSD databases shows that the cluster AB 2 X 37 occurs in 111 intermetallics belonging to 28 structure types.

The generation of possible crystal structures of primary amides

1983 ◽  
Vol 388 (1794) ◽  
pp. 133-175 ◽  
Keyword(s):  
Crystal Structures ◽  
Van Der Waals ◽  
Three Dimensional ◽  
Close Packing ◽  
Two Dimensional ◽  
Coulomb Interactions ◽  
Primary Amide ◽  
Size And Shape ◽  
Dimensional Crystal ◽  
Hydrogen Bonded

Procedures are outlined for generation of crystal structures of primary amide molecules by constructing the possible ways in which the molecules may pack. For each given one- or two-dimensional hydrogen-bonded array, ensembles of three-dimensional crystal structures are generated by considering the possible ways in which the arrays may be juxtaposed. Observed and generated hypothetical molecular arrangements are analysed to highlight both favourable and unfavourable features, par­ticularly in terms of close packing principles, the size and shape of the molecule, van der Waals and Coulomb interactions and N-H ∙ ∙ ∙ O bonding geometry.

scholarly journals Ambiguity of structure determination from a minimum of diffraction intensities

2014 ◽  
Vol 70 (4) ◽  
pp. 354-357 ◽  
Author(s):  
Ahmed Al-Asadi ◽  
Dimitri Leggas ◽  
Oleg V. Tsodikov
Keyword(s):  
Crystal Structures ◽  
Structure Determination ◽  
Three Dimensional ◽  
Minimum Data Set ◽  
Intensity Data ◽  
Data Set ◽  
One Dimensional ◽  
Minimum Data ◽  
Minimum Intensity ◽  
Dimensional Crystal

Although the ambiguity of the crystal structures determined directly from diffraction intensities has been historically recognized, it is not well understood in quantitative terms. Bernstein's theorem has recently been used to obtain the number of one-dimensional crystal structures of equal point atoms, given a minimum set of diffraction intensities. By a similar approach, the number of two- and three-dimensional crystal structures that can be determined from a minimum intensity data set is estimated herein. The ambiguity of structure determination from the algebraic minimum of data increases at least exponentially fast with the increasing structure size. Substituting lower-resolution intensities by higher-resolution ones in the minimum data set has little or no effect on this ambiguity if the number of such substitutions is relatively small.

scholarly journals Metastability relationship between two- and three-dimensional crystal structures: a case study of the Cu-based compounds

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shota Ono
Keyword(s):  
Crystal Structures ◽  
Three Dimensional ◽  
Building Blocks ◽  
Two Dimensional ◽  
3D Structures ◽  
Metallic Element ◽  
Computational Materials ◽  
Dynamics Simulations ◽  
Dimensional Crystal

AbstractSome of the three-dimensional (3D) crystal structures are constructed by stacking two-dimensional (2D) layers. To study whether this geometric concept, i.e., using 2D layers as building blocks for 3D structures, can be applied to computational materials design, we theoretically investigate the dynamical stability of copper-based compounds CuX (a metallic element X) in the B$$_h$$ h and L1$$_1$$ 1 structures constructed from the buckled honeycomb (BHC) structure and in the B2 and L1$$_0$$ 0 structures constructed from the buckled square (BSQ) structure. We demonstrate that (i) if CuX in the BHC structure is dynamically stable, those in the B$$_h$$ h and L1$$_1$$ 1 structures are also stable. Using molecular dynamics simulations, we particularly show that CuAu in the B$$_h$$ h and L1$$_1$$ 1 structures withstand temperatures as high as 1000 K. Although the interrelationship of the metastability between the BSQ and the 3D structures (B2 and L1$$_0$$ 0 ) is not clear, we find that (ii) if CuX in the B2 (L1$$_0$$ 0 ) structure is dynamically stable, that in the L1$$_0$$ 0 (B2) is unstable. This is rationalized by the tetragonal Bain path calculations.

Formation of three-dimensional colloidal crystals in a nematic liquid crystal

Soft Matter ◽  
2018 ◽  
Vol 14 (32) ◽  
pp. 6756-6766 ◽  
Author(s):  
Yiwei Wang ◽  
Pingwen Zhang ◽  
Jeff Z. Y. Chen
Keyword(s):  
Liquid Crystal ◽  
Crystal Structures ◽  
Nematic Liquid Crystal ◽  
Colloidal Particles ◽  
Three Dimensional ◽  
Colloidal Crystals ◽  
Dimensional Crystal

The overall three-dimensional crystal structures, formed by spherical colloids and liquid crystal molecules in the voids, are influenced by the size and the position of colloidal particles.

scholarly journals A cryoprotectant induces conformational change in glyceraldehyde-3-phosphate dehydrogenase

2018 ◽  
Vol 74 (5) ◽  
pp. 277-282 ◽  
Author(s):  
Yong Ju Kim
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Dna Replication ◽  
Membrane Fusion ◽  
Three Dimensional ◽  
Glycolytic Enzyme ◽  
Rna Transport ◽  
Nuclear Rna ◽  
Cellular Apoptosis ◽  
Dimensional Crystal

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a glycolytic enzyme, catalyses the conversion of D-glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate. While mammalian and yeast GAPDHs are multifunctional proteins that have additional functions beyond those involved in glycolysis, including reactions related to nuclear RNA transport, DNA replication/repair, membrane fusion and cellular apoptosis, Escherichia coli GAPDH (ecGAPDH) has only been reported to function in glycolysis. The S-loop of GAPDH is required for interaction with its cofactor and with other proteins. In this study, the three-dimensional crystal structure of GAPDH treated with trehalose is reported at 2.0 Å resolution. Trehalose was used as a cryoprotectant for the GAPDH crystals. The structure of trehalose-bound ecGAPDH was compared with the structures of both NAD+-free and NAD+-bound ecGAPDH. At the S-loop, the bound trehalose in the GAPDH structure induces a 2.4° rotation compared with the NAD+-free ecGAPDH structure and a 3.1° rotation compared with the NAD+-bound ecGAPDH structure.

scholarly journals SVAT4: a computer program for visualization and analysis of crystal structures

2020 ◽  
Vol 53 (3) ◽  
pp. 848-853
Author(s):  
X.-Z. Li
Keyword(s):  
Computer Program ◽  
Crystal Structures ◽  
Magnetic Moments ◽  
Three Dimensional ◽  
Data File ◽  
Software Suite ◽  
Wide Range ◽  
Range Of Functions ◽  
Diffraction Patterns ◽  
Dimensional Crystal

SVAT4 is a computer program for interactive visualization of three-dimensional crystal structures, including chemical bonds and magnetic moments. A wide range of functions, e.g. revealing atomic layers and polyhedral clusters, are available for further structural analysis. Atomic sizes, colors, appearance, view directions and view modes (orthographic or perspective views) are adjustable. Customized work for the visualization and analysis can be saved and then reloaded. SVAT4 provides a template to simplify the process of preparation of a new data file. SVAT4 can generate high-quality images for publication and animations for presentations. The usability of SVAT4 is broadened by a software suite for simulation and analysis of electron diffraction patterns.

Eight isostructural 4,4′-disubstitutedN-phenylbenzenesulfonamides

2012 ◽  
Vol 68 (10) ◽  
pp. o421-o426 ◽  
Author(s):  
Thomas Gelbrich ◽  
Terence L. Threlfall ◽  
Michael B. Hursthouse
Keyword(s):  
Crystal Structures ◽  
Phenyl Ring ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Dimensional Crystal ◽  
Hydrogen Bonded

The isostructural crystals of 4-cyano-N-(4-methoxyphenyl)benzenesulfonamide, C14H12N2O3S, (I),N-(4-methoxyphenyl)-4-(trifluoromethyl)benzenesulfonamide, C14H12F3NO3S, (II), 4-iodo-N-(4-methoxyphenyl)benzenesulfonamide, C13H12INO3S, (III), 4-bromo-N-(4-methoxyphenyl)benzenesulfonamide, C13H12BrNO3S, (IV), 4-chloro-N-(4-methoxyphenyl)benzenesulfonamide, C13H12ClNO3S, (V), 4-fluoro-N-(4-methoxyphenyl)benzenesulfonamide, C13H12FNO3S, (VI),N-(4-chlorophenyl)-4-methoxybenzenesulfonamide, C13H12ClNO3S, (VII), and 4-cyano-N-phenylbenzenesulfonamide, C13H10N2O2S, (VIII), contain infinite chains composed of N—H...O(sulfonyl) hydrogen-bonded molecules. The crystal structures of (I)–(VIII) have been compared using theXPac software and quantitative descriptors of isostructurality were generated [Gelbrich, Threlfall & Hursthouse (2012).CrystEngComm,14, 5454–5464]. Certain isostructural relationships in this series involve molecules with substantially different spatial demands,e.g.(VI) and (VIII) are related by the simultaneous interchange of F→CN on the benzenesulfonamide ring and OMe→H on theN-phenyl ring, which indicates that the geometry of the three-dimensional crystal-packing mode of (I)–(VIII) is unusually adaptable to different molecular shapes.

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