Crystallization and preliminary X-ray characterization of MutT2, MSMEG_5148 fromMycobacterium smegmatis

Crystallization of MutT2, MSMEG_5148 fromMycobacterium smegmatis, has been carried out and the crystals have been characterized using X-ray diffraction. Matthews coefficient calculation suggests the possibility of one protein molecule in the asymmetric unit of the orthorhombic unit cell, space groupP21212 orP2122. Solution of the structure of the protein by molecular replacement using the known three-dimensional structure of a bacterial Nudix hydrolase is envisaged.

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Purification, crystallization and preliminary X-ray diffraction analysis of theEscherichia colicommon pilus chaperone EcpB

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x15006354 ◽

2015 ◽

Vol 71 (6) ◽

pp. 676-679 ◽

Cited By ~ 1

Author(s):

James A. Garnett ◽

Mamou Diallo ◽

Steve J. Matthews

Keyword(s):

Heavy Atom ◽

Three Dimensional ◽

Solid Surfaces ◽

Dimensional Structure ◽

Molecular Replacement ◽

X Ray Diffraction ◽

X Ray ◽

Cell Parameters ◽

The Common ◽

First Time

Pili are key cell-surface components that allow the attachment of bacteria to both biological and abiotic solid surfaces, whilst also mediating interactions between themselves. InEscherichia coli, the common pilus (Ecp) belongs to an alternative chaperone–usher (CU) pathway that plays a major role in both early biofilm formation and host-cell adhesion. The chaperone EcpB is involved in the biogenesis of the filament, which is composed of EcpA and EcpD. Initial attempts at crystallizing EcpB using natively purified protein from the bacterial periplasm were not successful; however, after the isolation of EcpB under denaturing conditions and subsequent refolding, crystals were obtained at pH 8.0 using the sitting-drop method of vapour diffusion. Diffraction data have been processed to 2.4 Å resolution. These crystals belonged to the trigonal space groupP3121 orP3221, with unit-cell parametersa=b= 62.65,c= 121.14 Å and one monomer in the asymmetric unit. Molecular replacement was unsuccessful, but selenomethionine-substituted protein and heavy-atom derivatives are being prepared for phasing. The three-dimensional structure of EcpB will provide invaluable information on the subtle mechanistic differences in biogenesis between the alternative and classical CU pathways. Furthermore, this is the first time that this refolding strategy has been used to purify CU chaperones, and it could be implemented in similar systems where it has not been possible to obtain highly ordered crystals.

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MSMEG_6292, a Mycobacterium smegmatis RNA polymerase secondary channel-binding protein: purification, crystallization and X-ray diffraction analysis

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x18009755 ◽

2018 ◽

Vol 74 (9) ◽

pp. 543-548

Author(s):

Abyson Joseph ◽

Valakunja Nagaraja ◽

Ramanathan Natesh

Keyword(s):

Rna Polymerase ◽

Mycobacterium Smegmatis ◽

Transcriptional Activity ◽

Molecular Replacement ◽

X Ray Diffraction ◽

Secondary Channel ◽

X Ray ◽

Cell Parameters ◽

Crystallization Method ◽

Better Than

The transcriptional activity of RNA polymerase (RNAP) is controlled by a diverse set of regulatory factors. A subset of these regulators modulate the activity of RNAP through its secondary channel. Gre factors reactivate stalled elongation complexes by enhancing the intrinsic cleavage activity of RNAP. In the present study, the protein MSMEG_6292, a Gre-factor homologue from Mycobacterium smegmatis, was expressed heterologously in Escherichia coli and purified using standard chromatographic techniques. The hanging-drop vapour-diffusion crystallization method yielded diffraction-quality crystals. The crystals belonged to the trigonal space group P3121 (or its enantiomorph P3221), with unit-cell parameters a = b = 83.15, c = 107.07 Å, α = β = 90, γ = 120°. The crystals diffracted to better than 3.0 Å resolution. Molecular-replacement attempts did not yield any phasing models; hence, platinum derivatization was carried out with K2PtCl4 and derivative data were collected to 3.4 Å resolution.

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Structural characterization of quaternary selenites of tungsten(VI), A 2W3SeO12 (A = NH4, Cs, Rb, K or Tl)

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989021002735 ◽

2021 ◽

Vol 77 (4) ◽

pp. 406-411

Author(s):

Vineela Balisetty ◽

Kanamaluru Vidyasagar

Keyword(s):

Three Dimensional ◽

Spectroscopic Studies ◽

Solid State Reactions ◽

Dimensional Structure ◽

X Ray Diffraction ◽

Compound K ◽

Three Dimensional Structure ◽

Thermal And Spectroscopic Studies ◽

Anionic Framework

The quaternary A 2W3SeO12 (A = NH4, Cs, Rb, K or Tl) selenites have been prepared in the form of single crystals by hydrothermal and novel solid-state reactions. They were characterized by X-ray diffraction, thermal and spectroscopic studies. All of them have a hexagonal tungsten oxide (HTO) related [W3SeO12]2− anionic framework with pyramidally coordinated Se4+ ions. The known A 2W3SeO12 (A = NH4, Cs or Rb) compounds are isostructural with the Cs2W3TeO12 compound and have a non-centrosymmetric layered structure containing intra-layer Se—O bonds. The new compound K2W3SeO12(α) is isostructural with the K2W3TeO12 compound and has a centrosymmetric three-dimensional structure containing interlayer Se—O bonds. It is inferred that the new Tl2W3SeO12 compound has the same three-dimensional structure as K2W3SeO12(α).

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Three-dimensional X-ray diffraction imaging of process-induced dislocation loops in silicon

Journal of Applied Crystallography ◽

10.1107/s0021889811013264 ◽

2011 ◽

Vol 44 (3) ◽

pp. 526-531 ◽

Cited By ~ 7

Author(s):

David Allen ◽

Jochen Wittge ◽

Jennifer Stopford ◽

Andreas Danilewsky ◽

Patrick McNally

Keyword(s):

Semiconductor Industry ◽

Three Dimensional ◽

Crystal Defects ◽

Three Dimensions ◽

Dimensional Structure ◽

Dislocation Loops ◽

X Ray Diffraction ◽

X Ray ◽

Diffraction Imaging ◽

Relationship Of

In the semiconductor industry, wafer handling introduces micro-cracks at the wafer edge and the causal relationship of these cracks to wafer breakage is a difficult task. By way of understanding the wafer breakage process, a series of nano-indents were introduced both into 20 × 20 mm (100) wafer pieces and into whole wafers as a means of introducing controlled strain. Visualization of the three-dimensional structure of crystal defects has been demonstrated. The silicon samples were then treated by various thermal anneal processes to initiate the formation of dislocation loops around the indents. This article reports the three-dimensional X-ray diffraction imaging and visualization of the structure of these dislocations. A series of X-ray section topographs of both the indents and the dislocation loops were taken at the ANKA Synchrotron, Karlsruhe, Germany. The topographs were recorded on a CCD system combined with a high-resolution scintillator crystal and were measured by repeated cycles of exposure and sample translation along a direction perpendicular to the beam. The resulting images were then rendered into three dimensions utilizing open-source three-dimensional medical tomography algorithms that show the dislocation loops formed. Furthermore this technique allows for the production of a video (avi) file showing the rotation of the rendered topographs around any defined axis. The software also has the capability of splitting the image along a segmentation line and viewing the internal structure of the strain fields.

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Synthesis, Spectral, Structural and Thermal Characterization of Inorganic Crystal: Phenyl Trimethylammonium Tetrachlorocobaltate

Asian Journal of Chemistry ◽

10.14233/ajchem.2019.21929 ◽

2019 ◽

Vol 31 (8) ◽

pp. 1779-1784

Author(s):

V. Mohanraj ◽

R. Pavithra ◽

M. Thenmozhi ◽

R. Umarani

Keyword(s):

Three Dimensional ◽

Thermal Characterization ◽

Dimensional Structure ◽

X Ray Diffraction ◽

Monoclinic Crystal ◽

Evaporation Technique ◽

Ft Ir ◽

Thermal Stability Of ◽

Ft Ir Spectroscopy

Phenyl trimethylammonium tetrachlorocobaltate, crystals were grown by slow evaporation technique. The crystal was bright, transparent. The three dimensional structure of the phenyl trimethylammonium tetrachlorocobaltate was obtained from single crystal X-ray diffraction studies. The molecule belongs to monoclinic crystal system with C2/c space group. The presence of functional groups and modes of vibrations were identified by FT-IR spectroscopy. 1H NMR spectroscopy was also used to characterise the compound and the thermal stability of the crystal was established by TGA/DT analysis. This work undergoes phase transition which makes the study interesting.

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The three-dimensional structure of a class-Pi glutathione S-transferase complexed with glutathione: the active-site hydration provides insights into the reaction mechanism

Biochemical Journal ◽

10.1042/bj3330811 ◽

1998 ◽

Vol 333 (3) ◽

pp. 811-816 ◽

Cited By ~ 14

Author(s):

Antonio PÁRRAGA ◽

Isabel GARCÍA-SÁEZ ◽

Sinead B. WALSH ◽

Timothy J. MANTLE ◽

Miquel COLL

Keyword(s):

Conformational Changes ◽

Active Site ◽

Three Dimensional ◽

Dimensional Structure ◽

Water Molecules ◽

X Ray Diffraction ◽

Glutathione S Transferase ◽

X Ray ◽

The Right

The structure of mouse liver glutathione S-transferase P1-1 complexed with its substrate glutathione (GSH) has been determined by X-ray diffraction analysis. No conformational changes in the glutathione moiety or in the protein, other than small adjustments of some side chains, are observed when compared with glutathione adduct complexes. Our structure confirms that the role of Tyr-7 is to stabilize the thiolate by hydrogen bonding and to position it in the right orientation. A comparison of the enzyme–GSH structure reported here with previously described structures reveals rearrangements in a well-defined network of water molecules in the active site. One of these water molecules (W0), identified in the unliganded enzyme (carboxymethylated at Cys-47), is displaced by the binding of GSH, and a further water molecule (W4) is displaced following the binding of the electrophilic substrate and the formation of the glutathione conjugate. The possibility that one of these water molecules participates in the proton abstraction from the glutathione thiol is discussed.

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

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x14012746 ◽

2014 ◽

Vol 70 (8) ◽

pp. 1072-1075 ◽

Cited By ~ 1

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.

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Metal Ion-Driven Assembly of Two New Coordination Polymers Constructed by Asymmetric Tricarboxylate and Imidazole-Containing Ligands: Syntheses, Crystal Structures, and Luminescent Properties

Australian Journal of Chemistry ◽

10.1071/ch14127 ◽

2015 ◽

Vol 68 (1) ◽

pp. 121 ◽

Cited By ~ 2

Author(s):

Wenlong Liu ◽

Xueying Wang ◽

Mengqiang Wu ◽

Bing Wang

Keyword(s):

Infrared Spectroscopy ◽

Coordination Polymers ◽

Metal Ion ◽

Three Dimensional ◽

Luminescent Properties ◽

Dimensional Structure ◽

X Ray Diffraction ◽

Hydrothermal Conditions ◽

X Ray ◽

Dimethyl Benzene

Two new coordination polymers, namely, {[Cd3(bpt)2(bimb)2]·2(H2O)}n (1) and [Zn3(bpt)2(bimb)2]n (2) (bpt = biphenyl-3,4′,5-tricarboxylate, bimb = 1,4-bis(1-imidazol-yl)-2,5-dimethyl benzene), have been obtained under hydrothermal conditions. Their structures have been determined by single-crystal X-ray diffraction analysis and further characterised by elemental analysis and infrared spectroscopy. Complex 1 exhibits a trinodal (4,4,4)-connected topology with Schläfli symbol of (4.62.83)4.(64.82). Complex 2 is also a three-dimensional structure and displays a (3,4,6)-connected topology with Schläfli symbol of (4.62)2.(42.66.85.102).(64.82). It is shown that the asymmetrically tricarboxylate can bear diverse structures regulated by metal ions. The photoluminescence behaviours of compounds 1 and 2 were also discussed.

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Characterization of the structure and redox behaviour of cytochrome c3 from Desulfovibrio baculatus by 1H-nuclear-magnetic-resonance spectroscopy

Biochemical Journal ◽

10.1042/bj2940899 ◽

1993 ◽

Vol 294 (3) ◽

pp. 899-908 ◽

Cited By ~ 21

Author(s):

I B Coutinho ◽

D L Turner ◽

J LeGall ◽

A V Xavier

Keyword(s):

Chemical Shifts ◽

Three Dimensional ◽

Dimensional Structure ◽

Resonance Spectroscopy ◽

Cytochrome C3 ◽

X Ray ◽

1H Nuclear Magnetic Resonance ◽

Proton Resonances ◽

Nuclear Overhauser

Complete assignment of the aromatic and haem proton resonances in the cytochromes c3 isolated from Desulfovibrio baculatus strains (Norway 4, DSM 1741) and (DSM 1743) was achieved using one- and two-dimensional 1H n.m.r. Nuclear Overhauser enhancements observed between haem and aromatic resonances and between resonances due to different haems, together with the ring-current contributions to the chemical shifts of haem resonances, support the argument that the haem core architecture is conserved in the various cytochromes c3, and that the X-ray structure of the D. baculatus cytochrome c3 is erroneous. The relative orientation of the haems for both cytochromes was determined directly from n.m.r. data. The n.m.r. structures have a resolution of approximately 0.25 nm and are found to be in close agreement with the X-ray structure from D. vulgaris cytochrome c3. The proton assignments were used to relate the highest potential to a specific haem in the three-dimensional structure by monitoring the chemical-shift variation of several haem resonances throughout redox titrations followed by 1H n.m.r. The haem with highest redox potential is not the same as that in other cytochromes c3.

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