scholarly journals Crystallization and Preliminary X-ray Diffraction of a Halophilic Archaeal Malate Synthase

2009 ◽  
Vol 8 (2 and 3) ◽  
Author(s):  
Geoffrey Thomas ◽  
Kenneth Lamlenn ◽  
Bruce Howard
Keyword(s):  
Structural Information ◽  
Sequence Similarity ◽  
Three Dimensional ◽  
Halophilic Archaea ◽  
Crystal Form ◽  
Dead Sea ◽  
Malate Synthase ◽  
Metabolic Enzyme ◽  
X Ray Diffraction ◽  
X Ray

Malate synthases found in cells of the halophilic Archaea constitute a third isoform of this important metabolic enzyme, in addition to the well characterized A and G isoforms. They share little sequence similarity with these other two isoforms. Database searches using basic local alignments reveal relationships between isoforms A and G, but do not indicate a significant sequence relationship between members of this third isoform and those of isoform G, and only a distant relationship with members of isoform A. This third isoform, which we propose to call isoform H (Halophilic archaeal), is also significantly smaller in size: ~100 residues shorter than isoform A, and ~300 residues shorter than isoform G. Representatives of both isoform A and G have been structurally characterized, but no three-dimensional structural information exists for isoform H. Here we report the crystallization and preliminary X-ray diffraction from a crystal form of an H-isoform member, the malate synthase from the halophilic archaeon Haloferax volcanii, originally isolated from the mud of the Dead Sea. This crystal form diffracts well, and is amenable to single crystal X-ray analysis.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of a single variable domain of the immunoglobulin superfamily in amphioxus,Amphi-IgSF-V

2014 ◽  
Vol 70 (8) ◽  
pp. 1072-1075 ◽  
Author(s):  
Bo Jiang ◽  
Yanjie Liu ◽  
Rong Chen ◽  
Zhenbao Wang ◽  
Mansoor Tariq ◽  
...  
Keyword(s):  
Immune System ◽  
Structural Information ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Immunoglobulin Superfamily ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
System A ◽  
Human Immunoglobulins

Amphioxus is regarded as an essential animal model for the study of immune evolution. Discovery of new molecules with the immunoglobulin superfamily (IgSF) variable (V) domain in amphioxus would help in studying the evolution of IgSF V molecules in the immune system. A protein was found which just contains only one IgSF V domain in amphioxus, termedAmphi-IgSF-V; it has over 30% sequence identity to the V domains of human immunoglobulins and mammalian T-cell receptors. In order to clarify the three-dimensional structure of this new molecule in amphioxus,Amphi-IgSF-V was expressed, purified and crystallized, and diffraction data were collected to a resolution of 1.95 Å. The crystal belonged to space groupP3221, with unit-cell parametersa=b= 53.9,c= 135.5 Å. The Matthews coefficient and solvent content were calculated to be 2.58 Å3 Da−1and 52.38%, respectively. The results will provide structural information to study the evolution of IgSF V molecules in the immune system.

scholarly journals Methods for operando coherent X-ray diffraction of battery materials at the Advanced Photon Source

2019 ◽  
Vol 26 (1) ◽  
pp. 220-229 ◽  
Author(s):  
Luxi Li ◽  
Yingying Xie ◽  
Evan Maxey ◽  
Ross Harder
Keyword(s):  
Single Crystals ◽  
Electrode Material ◽  
Electrode Materials ◽  
Structural Information ◽  
Crystal Form ◽  
X Ray Diffraction ◽  
Diffractive Imaging ◽  
X Ray ◽  
The Individual ◽  
Photon Source

Bragg coherent X-ray diffraction imaging has become valuable for visualization of the structural, morphological and strain evolution of crystals in operando electrode materials. As the electrode material particles (either in a single-crystal form or an aggregation form of single crystals) are evenly dispersed and randomly oriented in the electrode laminate, the submicrometer-sized coherentX-ray beam can be used to probe the local properties of electrode material crystals using two approaches. Coherent multi-crystal diffraction provides collective structural information of phase transitions in tens of crystals simultaneously as well as the individual behavior from single crystals, which are oriented at the Bragg condition in the X-ray illumination volume. Bragg coherent diffractive imaging enables one to monitor the evolution of the morphology and strain in individual crystals. This work explores and highlights the Bragg coherent X-ray diffraction measurements of battery electrode materials in operando conditions at the 34-ID-C beamline at the Advanced Photon Source. The experiment is demonstrated with NaNi1/3Fe1/3Mn1/3O2, a sodium-ion cathode material loaded in a half cell. The paper will discuss, in detail, the beamline setup, sample mounting and handling, alignment strategies and the data acquisition protocols.

scholarly journals Crystal Structure of a Putative Modulator of Gyrase (TldE) from Thermococcus kodakarensis

Crystals ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 107 ◽  
Author(s):  
Xin Zhang ◽  
Zhengqun Li ◽  
Yanxiang Zhao ◽  
Xilan Cheng ◽  
Yang Liu ◽  
...  
Keyword(s):  
Metal Ion ◽  
Structural Information ◽  
Sequence Similarity ◽  
Dimensional Structure ◽  
Structural Basis ◽  
Diffusion Method ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Thermococcus Kodakarensis

TldD and TldE proteins interact and form a complex to degrade unfolded peptides. The gene Tk0499 from Thermococcus kodakarensis encoded a putative modulator of gyrase (TkTldE). Although TldE genes were common in bacteria and archaea, the structural basis on the evolution of proteins remained largely unknown. Here, the three-dimensional structure of TkTldE was determined by X-ray diffraction. Crystals were acquired by the sitting-drop vapor-diffusion method. X-ray diffraction data from crystals were collected at 2.35 Å. The space group and unit-cell parameters suggested that there were two molecules in the asymmetric unit. Our results showed that TkTldE forms a homodimer, which contained anti-parallel β-strands and a pair of α-helices. Comparison of the structures of TldE and TldD showed that despite their high sequence similarity, TldE lacked the conserved HExxxH and GxC motif in which two His and a Cys residues bound a metal ion. Taken together, these results provided insight into the structural information of this class of TldE/TldD.

Hard X-ray diffraction scanning tomography with sub-micrometre spatial resolution: application to an annealed γ-U0.85Mo0.15particle

2011 ◽  
Vol 44 (5) ◽  
pp. 1111-1119 ◽  
Author(s):  
Hervé Palancher ◽  
Rémi Tucoulou ◽  
Pierre Bleuet ◽  
Anne Bonnin ◽  
Eléonore Welcomme ◽  
...  
Keyword(s):  
Spatial Resolution ◽  
Structural Information ◽  
Three Dimensional ◽  
Real Space ◽  
Protective Role ◽  
Diffraction Tomography ◽  
X Ray Diffraction ◽  
X Ray ◽  
Thermally Activated

It is demonstrated that scanning X-ray diffraction tomography of heterogeneous and polycrystalline samples can provide real-space semi-quantitative three-dimensional structural information at a submicrometre spatial resolution. The capabilities of this technique are illustrated by the study of a slice of a spherical particle consisting of a UMo core (about 37 µm in diameter) surrounded by a UMoAl shell (5 µm thick). The technique allows precise characterization of the embedded UMo/UMoAl interface where the phases α-U (in the core), UAl2and U6Mo4Al43(in the shell) are found. Moreover, an unexpected phase (UC) is detected at a trace level. It is shown that the thickness of the UMoAl shell is locally anticorrelated with the amount of UC, suggesting that this phase plays a protective role in inhibiting thermally activated Al diffusion in UMo.

Structural chemistry of anionic fluoride and mixed-ligand fluoride complexes of indium(III)

2016 ◽  
Vol 36 (3) ◽  
Author(s):  
Ruven L. Davidovich ◽  
Pavel P. Fedorov ◽  
Artur I. Popov
Keyword(s):  
Structural Information ◽  
Three Dimensional ◽  
Outer Sphere ◽  
Mixed Ligand ◽  
X Ray Diffraction ◽  
Crystal Lattices ◽  
Coordination Polyhedra ◽  
X Ray ◽  
Cell Parameters ◽  
Fluoride Complexes

AbstractA total of 88 crystal lattice structures of indium(III) anionic fluoride and mixed-ligand fluoride complexes have been discussed and systematized. Most of these structures have been established by single-crystal X-ray diffraction techniques, but some were characterized by powder X-ray diffraction methods. The presented crystallography data were compared with known isotypical compounds. This paper offers a discussion of the geometry of indium and outer sphere cation coordination polyhedra; the association of indium atoms in dimer, oligomer, and polymer formations (chains, layers, frameworks); types of cation-anion interactions; and their contributions in actual three-dimensional crystal structures including types of the crystal lattices formed. We also used structural examples of potassium fluoroindates(III) to describe the basics of the structural depolymerization model for fluoride compounds, which is used to depict the formation and transformation of complex metal fluorides and predict structural types of novel or uncharacterized fluorides in the corresponding compound series. For the readers’ convenience, we have compiled structural information in a single table containing phase compositions and corresponding standard crystallographic data (such as crystal system, space group, unit cell parameters, number of formula units per cell [

scholarly journals On the accuracy and precision of X-ray and neutron diffraction results as a function of resolution and the electron density model

IUCrJ ◽  
2020 ◽  
Vol 7 (5) ◽  
pp. 920-933 ◽  
Author(s):  
W. Fabiola Sanjuan-Szklarz ◽  
Magdalena Woińska ◽  
Sławomir Domagała ◽  
Paulina M. Dominiak ◽  
Simon Grabowsky ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Oxalic Acid ◽  
Electron Density ◽  
Structural Information ◽  
Three Dimensional ◽  
Spherical Approximation ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atom Model ◽  
Accuracy And Precision

X-ray diffraction is the main source of three-dimensional structural information. In total, more than 1.5 million crystal structures have been refined and deposited in structural databanks (PDB, CSD and ICSD) to date. Almost 99.7% of them were obtained by approximating atoms as spheres within the independent atom model (IAM) introduced over a century ago. In this study, X-ray datasets for single crystals of hydrated α-oxalic acid were refined using several alternative electron density models that abandon the crude spherical approximation: the multipole model (MM), the transferable aspherical atom model (TAAM) and the Hirshfeld atom refinement (HAR) model as a function of the resolution of X-ray data. The aspherical models (MM, TAAM, HAR) give far more accurate and precise single-crystal X-ray results than IAM, sometimes identical to results obtained from neutron diffraction and at low resolution. Hence, aspherical approaches open new routes for improving existing structural information collected over the last century.

Ribosome Structural Organization

1974 ◽  
Vol 32 ◽  
pp. 332-333
Author(s):  
James A. Lake
Keyword(s):  
Ribosomal Proteins ◽  
Structural Organization ◽  
Three Dimensional ◽  
Small Subunit ◽  
Structural Studies ◽  
X Ray Diffraction ◽  
Specific Antibodies ◽  
X Ray ◽  
E Coli ◽  
Complete Sequences

The understanding of ribosome structure has advanced considerably in the last several years. Biochemists have characterized the constituent proteins and rRNA's of ribosomes. Complete sequences have been determined for some ribosomal proteins and specific antibodies have been prepared against all E. coli small subunit proteins. In addition, a number of naturally occuring systems of three dimensional ribosome crystals which are suitable for structural studies have been observed in eukaryotes. Although the crystals are, in general, too small for X-ray diffraction, their size is ideal for electron microscopy.

Direct visualization of phase-separated domains in lipid membranes

1978 ◽  
Vol 36 (2) ◽  
pp. 290-291
Author(s):  
S. W. Hui ◽  
T. P. Stewart
Keyword(s):  
Lipid Membranes ◽  
Structural Information ◽  
Freeze Fracture ◽  
Biological Molecules ◽  
Vacuum Drying ◽  
Direct Visualization ◽  
X Ray Diffraction ◽  
Electron Microscopic ◽  
X Ray ◽  
Hydrocarbon Chains

Direct electron microscopic study of biological molecules has been hampered by such factors as radiation damage, lack of contrast and vacuum drying. In certain cases, however, the difficulties may be overcome by using redundent structural information from repeating units and by various specimen preservation methods. With bilayers of phospholipids in which both the solid and fluid phases co-exist, the ordering of the hydrocarbon chains may be utilized to form diffraction contrast images. Domains of different molecular packings may be recgnizable by placing properly chosen filters in the diffraction plane. These domains would correspond to those observed by freeze fracture, if certain distinctive undulating patterns are associated with certain molecular packing, as suggested by X-ray diffraction studies. By using an environmental stage, we were able to directly observe these domains in bilayers of mixed phospholipids at various temperatures at which their phases change from misible to inmissible states.

Characterizations of Synthetic 8mol% YSZ with Comparison to 3mol %YSZ for HT-SOFC

2020 ◽  
Vol 38 (4A) ◽  
pp. 491-500
Author(s):  
Abeer F. Al-Attar ◽  
Saad B. H. Farid ◽  
Fadhil A. Hashim
Keyword(s):  
Ionic Conductivity ◽  
Electrochemical Impedance ◽  
Structural Information ◽  
Impedance Analysis ◽  
High Energy ◽  
Yttria Stabilized Zirconia ◽  
X Ray Diffraction ◽  
Stabilized Zirconia ◽  
Powder Morphology ◽  
X Ray

In this work, Yttria (Y2O3) was successfully doped into tetragonal 3mol% yttria stabilized Zirconia (3YSZ) by high energy-mechanical milling to synthesize 8mol% yttria stabilized Zirconia (8YSZ) used as an electrolyte for high temperature solid oxide fuel cells (HT-SOFC). This work aims to evaluate the densification and ionic conductivity of the sintered electrolytes at 1650°C. The bulk density was measured according to ASTM C373-17. The powder morphology and the microstructure of the sintered electrolytes were analyzed via Field Emission Scanning Electron Microscopy (FESEM). The chemical analysis was obtained with Energy-dispersive X-ray spectroscopy (EDS). Also, X-ray diffraction (XRD) was used to obtain structural information of the starting materials and the sintered electrolytes. The ionic conductivity was obtained through electrochemical impedance spectroscopy (EIS) in the air as a function of temperatures at a frequency range of 100(mHz)-100(kHz). It is found that the 3YSZ has a higher density than the 8YSZ. The impedance analysis showed that the ionic conductivity of the prepared 8YSZ at 800°C is0.906 (S.cm) and it was 0.214(S.cm) of the 3YSZ. Besides, 8YSZ has a lower activation energy 0.774(eV) than that of the 3YSZ 0.901(eV). Thus, the prepared 8YSZ can be nominated as an electrolyte for the HT-SOFC.

scholarly journals An investigation of polyhedral deformation in two mixed-metal diarsenates: SrZnAs2O7and BaCuAs2O7

2015 ◽  
Vol 71 (4) ◽  
pp. 330-337 ◽  
Author(s):  
Sabina Kovač ◽  
Ljiljana Karanović ◽  
Tamara Đorđević
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
General Formula ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
Hydrothermal Conditions ◽  
X Ray ◽  
Open Framework ◽  
Geometrical Characteristics ◽  
Barium Copper

Two isostructural diarsenates, SrZnAs2O7(strontium zinc diarsenate), (I), and BaCuAs2O7[barium copper(II) diarsenate], (II), have been synthesized under hydrothermal conditions and characterized by single-crystal X-ray diffraction. The three-dimensional open-framework crystal structure consists of corner-sharingM2O5(M2 = Zn or Cu) square pyramids and diarsenate (As2O7) groups. Each As2O7group shares its five corners with five differentM2O5square pyramids. The resulting framework delimits two types of tunnels aligned parallel to the [010] and [100] directions where the large divalent nine-coordinatedM1 (M1 = Sr or Ba) cations are located. The geometrical characteristics of theM1O9,M2O5and As2O7groups of known isostructural diarsenates, adopting the general formulaM1IIM2IIAs2O7(M1II= Sr, Ba, Pb;M2II= Mg, Co, Cu, Zn) and crystallizing in the space groupP21/n, are presented and discussed.

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