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

1998 ◽  
Vol 333 (3) ◽  
pp. 811-816 ◽  
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.

Diffuse scattering in protein crystallography

1995 ◽  
Vol 28 (2) ◽  
pp. 131-169 ◽  
Author(s):  
Jean-Pierre Benoit ◽  
Jean Doucet
Keyword(s):  
Molecular Biology ◽  
Active Site ◽  
Diffuse Scattering ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Physico Chemical ◽  
Chemical Conditions ◽  
Functional Mechanisms

The understanding of flexibility and deformability in proteins is one of the current major challenges of structural molecular biology. The knowledge of the average atomic positions of three-dimensional folding of proteins, which is obtained either by X-ray diffraction or n.m.r. spectroscopy, is generally not sufficient to explain their functional mechanisms. Very often it is necessary to consider the existence of other concerted atomic motions as, for example, in the well-known case of the CO molecule fixation at the active site of myoglobin which requires the concerted displacement of a large number of atoms in order to open a channel down to this site. This opening, which depends on the physico-chemical conditions, plays the role of a regulator in the biochemical reactions (Janin & Wodak, 1983; Tainer et al. 1984; Westhof et al. 1984; Ormos et al. 1988).

A novel alkaline earth strontium(II) coordination polymer: poly[hexaaquatetrakis(μ5-pyridine-2,6-dicarboxylato)bis(μ4-pyridine-2,6-dicarboxylato)(μ7-sulfato)heptastrontium(II)]

2014 ◽  
Vol 70 (6) ◽  
pp. 584-587 ◽  
Author(s):  
Wei Zhang ◽  
Shu-Guang Qi ◽  
Yu-Quan Feng
Keyword(s):  
Coordination Polymer ◽  
Coordination Mode ◽  
Alkaline Earth ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
Stacking Interactions ◽  
X Ray Diffraction ◽  
Sulfate Anion ◽  
X Ray

The title compound, [Sr7(C7H3NO4)6(SO4)(H2O)6]n, has been synthesized by an ionothermal method using the ionic liquid 1-ethyl-3-methylimidazolium ([Emim]Br) as solvent, and characterized by elemental analysis, energy-dispersive X-ray spectroscopy, IR and single-crystal X-ray diffraction. The structure of the compound can be viewed as a three-dimensional coordination polymer composed of Sr2+cations, pyridine-2,6-dicarboxylate anions, sulfate anions and water molecules. The compound not only exhibits a three-dimensional structure with a unique coordination mode of the sulfate anion, but also features the first example of a heptanuclear strontium(II) coordination polymer. The structure is further stabilized by O—H...O hydrogen bonds and π–π stacking interactions.

SdsA polymorph isolation and improvement of their crystal quality using nonconventional crystallization techniques

2015 ◽  
Vol 48 (5) ◽  
pp. 1551-1559 ◽  
Author(s):  
Eugenio De la Mora ◽  
Edith Flores-Hernández ◽  
Jean Jakoncic ◽  
Vivian Stojanoff ◽  
Dritan Siliqi ◽  
...  
Keyword(s):  
Magnetic Field ◽  
Active Site ◽  
Crystal Packing ◽  
Sodium Dodecyl ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
Oligomeric State ◽  
X Ray ◽  
Internal Order

SdsA, a sodium dodecyl sulfate hydrolase, fromPseudomonas aeruginosawas crystallized in three different crystal polymorphs and their three-dimensional structure was determined. The different polymorphs present different crystal packing habits. One of the polymorphs suggests the existence of a tetramer, an oligomeric state not observed previously, while the crystal packing of the remaining two polymorphs obstructs the active site entrance but stabilizes flexible regions of the protein. Nonconventional crystallization methods that minimize convection, such as counterdiffusion in polyvinyl alcohol gel coupled with the influence of a 500 MHz (10.2 T) magnetic field, were necessary to isolate the poorest diffracting polymorph and increase its internal order to determine its structure by X-ray diffraction. The results obtained show the effectiveness of nonconventional crystallographic methods to isolate different crystal polymorphs.

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

2011 ◽  
Vol 44 (3) ◽  
pp. 526-531 ◽  
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.

scholarly journals Synthesis, Structures and Electrochemical Properties of Lithium 1,3,5-Benzenetricarboxylate Complexes

Polymers ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 126 ◽  
Author(s):  
Pei-Chi Cheng ◽  
Bing-Han Li ◽  
Feng-Shuen Tseng ◽  
Po-Ching Liang ◽  
Chia-Her Lin ◽  
...  
Keyword(s):  
Electrochemical Properties ◽  
Electrode Materials ◽  
Three Dimensional ◽  
Lithium Ion ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
One Dimensional ◽  
X Ray ◽  
Crystal Transformation ◽  
Discharge Capacities

Four lithium coordination polymers, [Li3(BTC)(H2O)6] (1), [Li3(BTC)(H2O)5] (2), [Li3(BTC)(μ2-H2O)] (3), and [Li(H2BTC)(H2O)] (4) (H3BTC = 1,3,5-benzenetricarboxylatic acid), have been synthesized and characterized. All the structures have been determined using single crystal X-ray diffraction studies. Complexes 1 and 2 have two-dimensional (2-D) sheets, whereas complex 3 has three-dimensional (3-D) frameworks and complex 4 has one-dimensional (1-D) tubular chains. The crystal-to-crystal transformation was observed in 1–3 upon removal of water molecules, which accompanied the changes in structures and ligand bridging modes. Furthermore, the electrochemical properties of complexes 3 and 4 have been studied to evaluate these compounds as electrode materials in lithium ion batteries with the discharge capacities of 120 and 257 mAhg−1 in the first thirty cycles, respectively.

scholarly journals Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

2018 ◽  
Vol 19 (11) ◽  
pp. 3401 ◽  
Author(s):  
Ashutosh Srivastava ◽  
Tetsuro Nagai ◽  
Arpita Srivastava ◽  
Osamu Miyashita ◽  
Florence Tama
Keyword(s):  
Protein Dynamics ◽  
Computational Methods ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Insight Into

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.

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.

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

2015 ◽  
Vol 68 (1) ◽  
pp. 121 ◽  
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.

A novel dinuclear bismuth(III) coordination compound: bis(μ-pyridine-2,6-dicarboxylato)-κ4O2,N,O6:O6′;κ4O2:O2′,N,O6-bis[(azido-κN)(1,10-phenanthroline-κ2N,N′)bismuth(III)] tetrahydrate

2014 ◽  
Vol 70 (6) ◽  
pp. 562-565 ◽  
Author(s):  
Wei Zhang ◽  
Yu-Quan Feng
Keyword(s):  
Molecular Structure ◽  
Hydrogen Bonds ◽  
Coordination Compound ◽  
Photoelectron Spectroscopy ◽  
Three Dimensional ◽  
Water Molecules ◽  
Stacking Interactions ◽  
Coordination Geometry ◽  
X Ray Diffraction ◽  
X Ray

A novel dinuclear bismuth(III) coordination compound, [Bi2(C7H3NO4)2(N3)2(C12H8N2)2]·4H2O, has been synthesized by an ionothermal method and characterized by elemental analysis, energy-dispersive X-ray spectroscopy, IR, X-ray photoelectron spectroscopy and single-crystal X-ray diffraction. The molecular structure consists of one centrosymmetric dinuclear neutral fragment and four water molecules. Within the dinuclear fragment, each BiIIIcentre is seven-coordinated by three O atoms and four N atoms. The coordination geometry of each BiIIIatom is distorted pentagonal–bipyramidal (BiO3N4), with one azide N atom and one bridging carboxylate O atom located in axial positions. The carboxylate O atoms and water molecules are assembledviaO—H...O hydrogen bonds, resulting in the formation of a three-dimensional supramolecular structure. Two types of π–π stacking interactions are found, with centroid-to-centroid distances of 3.461 (4) and 3.641 (4) Å.

A one-dimensional coordination polymer with a three-dimensional supramolecular framework:catena-poly[[[(3,4,7,8-tetramethyl-1,10-phenanthroline)cadmium(II)]-μ3-4,4′-sulfonyldibenzoato] trihydrate]

2013 ◽  
Vol 69 (3) ◽  
pp. 241-243 ◽  
Author(s):  
Jun Wang ◽  
Jian-Qing Tao ◽  
Xiao-Juan Xu ◽  
Chun-Yun Tan
Keyword(s):  
Three Dimensional ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Polymeric Compound ◽  
Chain Polymer ◽  
One Dimensional ◽  
X Ray ◽  
Carboxylate Groups ◽  
Metal Organic ◽  
Coordination Patterns

In the title mixed-ligand metal–organic polymeric compound, {[Cd(C14H8O6S)(C16H16N2)]·3H2O}n, the asymmetric unit contains a crystallographically unique CdIIatom, one doubly deprotonated 4,4′-sulfonyldibenzoic acid (H2SDBA) ligand, one 3,4,7,8-tetramethyl-1,10-phenanthroline (TMPHEN) molecule and three solvent water molecules. Each CdIIcentre is six-coordinated by two O atoms from a chelating carboxylate group of a SDBA2−ligand, two O atoms from monodentate carboxylate groups of two different SDBA2−ligands and two N atoms from a chelating TMPHEN ligand. There are two coordination patterns for the carboxylate groups of the SDBA2−ligand, with one in a μ1-η1:η1chelating mode and the other in a μ2-η1:η1bis-monodentate mode. Single-crystal X-ray diffraction analysis revealed that the title compound is a one-dimensional double-chain polymer containing 28-membered rings based on the [Cd2(CO2)2] rhomboid subunit. More interestingly, a chair-shaped water hexamer cluster is observed in the compound.

Sign in / Sign up

Export Citation Format

Share Document