scholarly journals The structure of an iron-containing alcohol dehydrogenase from a hyperthermophilic archaeon in two chemical states

2019 ◽  
Vol 75 (4) ◽  
pp. 217-226
Author(s):  
Steven B. Larson ◽  
Jesse A. Jones ◽  
Alexander McPherson
Keyword(s):  
Alcohol Dehydrogenase ◽  
Symmetry Axis ◽  
Thermotoga Maritima ◽  
Molecular Replacement ◽  
Nucleotide Binding Domain ◽  
Hyperthermophilic Archaeon ◽  
Space Groups ◽  
Tetragonal Crystals ◽  
Unit Cells ◽  
Chemical States

An iron-containing alcohol dehydrogenase (FeADH) from the hyperthermophilic archaeonThermococcus thioreducenswas crystallized in unit cells belonging to space groupsP21,P212121andP43212, and the crystal structures were solved at 2.4, 2.1 and 1.9 Å resolution, respectively, by molecular replacement using the FeADH fromThermotoga maritima(Schwarzenbacheret al., 2004) as a model. In the monoclinic and orthorhombic crystals the dehydrogenase (molecular mass 41.5 kDa) existed as a dimer containing a twofold noncrystallographic symmetry axis, which was crystallographic in the tetragonal crystals. In the monoclinic and orthorhombic asymmetric units one molecule contained iron and an NADP molecule, while the other did not. The tetragonal crystals lacked both iron and NADP. The structure is very similar to that of the FeADH fromT. maritima(average r.m.s. difference for Cαatoms of 1.8 Å for 341 aligned atoms). The iron, which is internally sequestered, is bound entirely by amino acids from one domain: three histidines and one aspartic acid. The coenzyme is in an extended conformation, a feature that is common to the large superfamily of NADH-dependent dehydrogenases that share a classical nucleotide-binding domain. A long broad tunnel passes entirely through the enzyme between the two domains, completely encapsulating the coenzyme.

Crystal chemistry of transition metal diarsenates M 2As2O7 (M = Mn, Co, Ni, Zn): variants of the thortveitite structure

2010 ◽  
Vol 66 (6) ◽  
pp. 603-614 ◽  
Author(s):  
Matthias Weil ◽  
Berthold Stöger
Keyword(s):  
Crystal Structure ◽  
Low Temperature ◽  
Transition Metal ◽  
Basic Structure ◽  
Structure Type ◽  
Ambient Conditions ◽  
Modulated Structure ◽  
Triclinic Crystal System ◽  
Space Groups ◽  
Unit Cells

The structures of the 3d divalent transition-metal diarsenates M 2As2O7 (M = Mn, Co, Ni, Zn) can be considered as variants of the monoclinic (C2/m) thortveitite [Sc2Si2O7] structure type with a ≃ 6.7, b ≃ 8.5, c ≃ 4.7 Å, α ≃ 90, β ≃ 102, γ ≃ 90° and Z = 2. Co2As2O7 and Ni2As2O7 are dimorphic. Their high-temperature (β) polymorphs adopt the thortveitite aristotype structure in C2/m, whereas their low-temperature (α) polymorphs are hettotypes and crystallize with larger unit cells in the triclinic crystal system in space groups P\bar 1 and P1, respectively. Mn2As2O7 undergoes no phase transition and likewise adopts the thortveitite structure type in C2/m. Zn2As2O7 has an incommensurately modulated crystal structure [C2/m(α,0,γ)0s] with q = [0.3190 (1), 0, 0.3717 (1)] at ambient conditions and transforms reversibly to a commensurately modulated structure with Z = 12 (I2/c) below 273 K. The Zn phase resembles the structures and phase transitions of Cr2P2O7. Besides descriptions of the low-temperature Co2As2O7, Ni2As2O7 and Zn2As2O7 structures as five-, three- and sixfold superstructures of the thortveitite-type basic structure, the superspace approach can also be applied to descriptions of all the commensurate structures. In addition to the ternary M 2As2O7 phases, the quaternary phase (Ni,Co)2As2O7 was prepared and structurally characterized. In contrast to the previously published crystal structure of the mineral petewilliamsite, which has the same idealized formula and has been described as a 15-fold superstructure of the thortveitite-type basic structure in space group C2, synthetic (Ni,Co)2As2O7 can be considered as a solid solution adopting the α-Ni2As2O7 structure type. Differences of the two structure models for (Ni,Co)2As2O7 are discussed.

scholarly journals Genetic and biochemical characterization of a short-chain alcohol dehydrogenase from the hyperthermophilic archaeon Pyrococcus furiosu s

2001 ◽  
Vol 268 (10) ◽  
pp. 3062-3068 ◽  
Author(s):  
John van der Oost ◽  
Wilfried G. B. Voorhorst ◽  
Servé W. M. Kengen ◽  
Ans C. M. Geerling ◽  
Vincent Wittenhorst ◽  
...  
Keyword(s):  
Alcohol Dehydrogenase ◽  
Biochemical Characterization ◽  
Short Chain ◽  
Chain Alcohol ◽  
Hyperthermophilic Archaeon ◽  
Short Chain Alcohol

Mathematical aspects of molecular replacement. IV. Measure-theoretic decompositions of motion spaces

2017 ◽  
Vol 73 (5) ◽  
pp. 387-402 ◽  
Author(s):  
Gregory S. Chirikjian ◽  
Sajdeh Sajjadi ◽  
Bernard Shiffman ◽  
Steven M. Zucker
Keyword(s):  
General Theory ◽  
Rigid Body ◽  
Three Dimensional ◽  
Molecular Replacement ◽  
Translation Group ◽  
Common Occurrence ◽  
Space Group ◽  
Space Groups ◽  
Relevant Case ◽  
The Subject

In molecular-replacement (MR) searches, spaces of motions are explored for determining the appropriate placement of rigid-body models of macromolecules in crystallographic asymmetric units. The properties of the space of non-redundant motions in an MR search, called a `motion space', are the subject of this series of papers. This paper, the fourth in the series, builds on the others by showing that when the space group of a macromolecular crystal can be decomposed into a product of two space subgroups that share only the lattice translation group, the decomposition of the group provides different decompositions of the corresponding motion spaces. Then an MR search can be implemented by trading off between regions of the translation and rotation subspaces. The results of this paper constrain the allowable shapes and sizes of these subspaces. Special choices result when the space group is decomposed into a product of a normal Bieberbach subgroup and a symmorphic subgroup (which is a common occurrence in the space groups encountered in protein crystallography). Examples of Sohncke space groups are used to illustrate the general theory in the three-dimensional case (which is the relevant case for MR), but the general theory in this paper applies to any dimension.

TheComputational Crystallography Toolbox: crystallographic algorithms in a reusable software framework

2002 ◽  
Vol 35 (1) ◽  
pp. 126-136 ◽  
Author(s):  
Ralf W. Grosse-Kunstleve ◽  
Nicholas K. Sauter ◽  
Nigel W. Moriarty ◽  
Paul D. Adams
Keyword(s):  
Structural Genomics ◽  
Macromolecular Structure ◽  
Software Framework ◽  
Software Components ◽  
Software Developers ◽  
Space Groups ◽  
Reusable Software ◽  
New Methods ◽  
Structure Solution ◽  
Unit Cells

The advent of structural genomics initiatives has led to a pressing need for high-throughput macromolecular structure determination. To accomplish this, new methods and inevitably new software must be developed to accelerate the process of structure solution. To minimize duplication of effort and to generate maintainable code efficiently, a toolbox of basic crystallographic software components is required. The development of theComputational Crystallography Toolbox(cctbx) has been undertaken for this purpose. In this paper, the fundamental requirements for thecctbxare outlined and the decisions that have lead to its implementation are explained. Thecctbxcurrently contains algorithms for the handling of unit cells, space groups and atomic scatterers, and is released under an Open Source license to allow unrestricted use and continued development. It will be developed further to become a comprehensive library of crystallographic tools useful to the entire community of software developers.

scholarly journals The unit cells and space groups of SeCl4and TeCl4

1964 ◽  
Vol 17 (6) ◽  
pp. 756-756 ◽  
Author(s):  
A. W. Cordes ◽  
R. F. Kruh ◽  
E. K. Gordon ◽  
M. K. Kemp
Keyword(s):  
Space Groups ◽  
Unit Cells

Fundamentals of crystallography

2013 ◽  
Author(s):  
Carmelo Giacovazzo
Keyword(s):  
Unit Cell ◽  
Generic Point ◽  
Cell Content ◽  
Daily Work ◽  
Space Groups ◽  
Crystallographic Symmetry ◽  
Unit Cells ◽  
Basic Concepts ◽  
Periodic Repetition ◽  
Unit Vectors

In this chapter we summarize the basic concepts, formulas and tables which constitute the essence of general crystallography. In Sections 1.2 to 1.5 we recall, without examples, definitions for unit cells, lattices, crystals, space groups, diffraction conditions, etc. and their main properties: reading these may constitute a useful reminder and support for daily work. In Section 1.6 we establish and discuss the basic postulate of structural crystallography: this was never formulated, but during any practical phasing process it is simply assumed to be true by default. We will also consider the consequences of such a postulate and the caution necessary in its use. We recall the main concepts and definitions concerning crystals and crystallographic symmetry. Crystal. This is the periodic repetition of a motif (e.g. a collection of molecules, see Fig. 1.1). An equivalent mathematical definition is: the crystal is the convolution between a lattice and the unit cell content (for this definition see (1.4) below in this section). Unit cell. This is the parallelepiped containing the motif periodically repeated in the crystal. It is defined by the unit vectors a, b, c, or, by the six scalar parameters a, b, c, α, β, γ (see Fig. 1.1). The generic point into the unit cell is defined by the vector . . . r = x a + y b + z c, . . . where x, y, z are fractional coordinates (dimensionless and lying between 0 and 1). The volume of the unit cell is given by (see Fig. 1.2) . . . V = a ∧ b · c = b ∧ c · a = c ∧ a · b. (1.1). . .

Atomic resolution structure of a chimeric DNA–RNA Z-type duplex in complex with Ba2+ions: a case of complicated multi-domain twinning

2016 ◽  
Vol 72 (2) ◽  
pp. 211-223 ◽  
Author(s):  
Miroslaw Gilski ◽  
Pawel Drozdzal ◽  
Ryszard Kierzek ◽  
Mariusz Jaskolski
Keyword(s):  
Molecular Replacement ◽  
Higher Symmetry ◽  
Barium Ions ◽  
Space Groups ◽  
Left Handed ◽  
Crystal Twinning ◽  
Using Data ◽  
High Degree ◽  
Packing Analysis ◽  
Resolution Structure

The self-complementary dCrGdCrGdCrG hexanucleotide, in which not only the pyrimidine/purine bases but also the ribo/deoxy sugars alternate along the sequence, was crystallized in the presence of barium cations in the form of a left-handed Z-type duplex. The asymmetric unit of theP21crystal with a pseudohexagonal lattice contains four chimeric duplexes and 16 partial Ba2+sites. The chimeric (DNA–RNA)2duplexes have novel patterns of hydration and exhibit a high degree of discrete conformational disorder of their sugar-phosphate backbones, which can at least partly be correlated with the fractional occupancies of the barium ions. The crystals of the DNA–RNA chimeric duplex in complex with Ba2+ions and also with Sr2+ions exhibit complicated twinning, which in combination with structural pseudosymmetry made structure determination difficult. The structure could be successfully solved by molecular replacement in space groupsP1 andP21but not in orthorhombic or higher symmetry and, after scrupulous twinning and packing analysis, was refined in space groupP21to anRandRfreeof 11.36 and 16.91%, respectively, using data extending to 1.09 Å resolution. With the crystal structure having monoclinic symmetry, the sixfold crystal twinning is a combination of threefold and twofold rotations. The paper describes the practical aspects of dealing with cases of complicated twinning and pseudosymmetry, and compares the available software tools for the refinement and analysis of such cases.

Mathematical aspects of molecular replacement. III. Properties of space groups preferred by proteins in the Protein Data Bank

2015 ◽  
Vol 71 (2) ◽  
pp. 186-194 ◽  
Author(s):  
G. Chirikjian ◽  
S. Sajjadi ◽  
D. Toptygin ◽  
Y. Yan
Keyword(s):  
Rigid Body ◽  
Protein Data Bank ◽  
Data Bank ◽  
Continuous Group ◽  
Molecular Replacement ◽  
Macromolecular Crystallography ◽  
Coset Space ◽  
Space Groups ◽  
The Third ◽  
Rigid Body Motions

The main goal of molecular replacement in macromolecular crystallography is to find the appropriate rigid-body transformations that situate identical copies of model proteins in the crystallographic unit cell. The search for such transformations can be thought of as taking place in the coset space Γ\Gwhere Γ is the Sohncke group of the macromolecular crystal andGis the continuous group of rigid-body motions in Euclidean space. This paper, the third in a series, is concerned with viewing nonsymmorphic Γ in a new way. These space groups, rather than symmorphic ones, are the most common ones for protein crystals. Moreover, their properties impact the structure of the space Γ\G. In particular, nonsymmorphic space groups contain both Bieberbach subgroups and symmorphic subgroups. A number of new theorems focusing on these subgroups are proven, and it is shown that these concepts are related to the preferences that proteins have for crystallizing in different space groups, as observed in the Protein Data Bank.

Structure and spectroscopic properties of (AA′)(BB′)O3 mixed-perovskite crystals

2005 ◽  
Vol 20 (12) ◽  
pp. 3329-3337 ◽  
Author(s):  
Dorota A. Pawlak ◽  
Masahiko Ito ◽  
Lukasz Dobrzycki ◽  
Krzysztof Wozniak ◽  
Masaoki Oku ◽  
...  
Keyword(s):  
Spectroscopic Properties ◽  
Regular System ◽  
Interstitial Oxygen ◽  
X Ray Diffraction ◽  
Absorption Bands ◽  
Space Groups ◽  
Oxygen Ions ◽  
Reducing Atmosphere ◽  
Lanthanum Strontium ◽  
Unit Cells

Five different mixed-perovskite (AA′)(BB′)O3 single crystals were grown, where A = La, Nd; A′ = Sr; B = Al, Ga; and B′ = Ta, Nb. The as-grown crystals were yellowish/brownish. After annealing in air, the coloration was more intense. Annealing in a reducing atmosphere decreased coloration. The crystals were investigated by transmission spectroscopy, electron spectroscopy for chemical analysis (ESCA), and single-crystal x-ray diffraction. Additional broad absorption bands in the transmission spectra were observed for the as-grown samples. They are in line with the changes of the shape of O(1s) ESCA peaks. Redundant interstitial oxygen ions were recognized as the reason for the crystal coloration. All structures were solved and refined in different space groups of the regular system. Some of the unit cells have a doubled lattice constant: (i) lanthanum strontium gallium niobate, Pm3m, 3.9323(5) Å, at 100 K, 3.9270(5) Å; (ii) neodymium strontium aluminum tantalate, Pm3m, 3.8353(4) Å; (iii) lanthanum strontium aluminum tantalate, Pn3m, 7.720(1) Å, annealed in reducing atmosphere, 7.708(1) Å; (iv) neodymium strontium aluminum niobate, Fm3m, 7.744(4) Å.

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