scholarly journals Cloning, purification, crystallization and preliminary X-ray diffraction crystallographic study of acyl-protein thioesterase 1 fromSaccharomyces cerevisiae

2012 ◽  
Vol 68 (7) ◽  
pp. 775-777
Author(s):  
Ye Yuan ◽  
Xiao Wang ◽  
Xu Li ◽  
Maikun Teng ◽  
Liwen Niu ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Modification ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Crystallographic Study ◽  
Preliminary Model

Palmitoylation/depalmitoylation plays an important role in protein modification. yApt1 is the only enzyme inSaccharomyces cerevisiaethat catalyses depalmitoylation. In the present study, recombinant full-length yApt1 was cloned, expressed, purified and crystallized. The crystals diffracted to 2.40 Å resolution and belonged to space groupP42212, with unit-cell parametersa = b = 146.43,c = 93.29 Å. A preliminary model of the three-dimensional structure has been built and further refinement is ongoing.

scholarly journals Crystallization and preliminary crystallographic analysis of LipC12, a true lipase isolated through a metagenomics approach

2012 ◽  
Vol 68 (2) ◽  
pp. 175-177 ◽  
Author(s):  
V. P. Martini ◽  
A. Glogauer ◽  
J. Iulek ◽  
E. M. Souza ◽  
F. O. Pedrosa ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Three Dimensional ◽  
Sodium Formate ◽  
Crystallographic Analysis ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Sequence Identity

LipC12, a true lipase from family I.1 of bacterial lipases which was previously isolated through a metagenomics approach, contains 293 amino acids. Among lipases of known three-dimensional structure, it has a sequence identity of 47% to the lipase fromPseudomonas aeruginosaPAO1. Recombinant N-terminally His6-tagged LipC12 protein was expressed inEscherichia coli, purified in a homogenous form and crystallized in several conditions, with the best crystals being obtained using 2.0 Msodium formate and 0.1 Mbis-tris propane pH 7.0. X-ray diffraction data were collected to 2.70 Å resolution. The crystals belonged to the tetragonal space groupP4122, with unit-cell parametersa=b= 58.62,c = 192.60 Å.

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 Crystallization and preliminary crystallographic studies of PotA, a membrane-associated ATPase of the spermidine-preferential uptake system inThermotoga maritima

2014 ◽  
Vol 70 (6) ◽  
pp. 738-741 ◽  
Author(s):  
Shigeru Sugiyama ◽  
Keiko Kashiwagi ◽  
Keisuke Kakinouchi ◽  
Hideyuki Tomitori ◽  
Ken Kanai ◽  
...  
Keyword(s):  
Thermotoga Maritima ◽  
Three Dimensional ◽  
Crystallographic Analysis ◽  
Uptake System ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Polyamine Uptake ◽  
Preferential Uptake

A membrane-associated ATPase, PotA, is a component of the spermidine-preferential uptake system in prokaryotes that plays an important role in normal cell growth by regulating the cellular polyamine concentration. No three-dimensional structures of membrane-associated ATPases in polyamine-uptake systems have been determined to date. Here, the crystallization and preliminary X-ray diffraction analysis of PotA fromThermotoga maritimaare reported. Diffraction data were collected and processed to 2.7 Å resolution from both native and selenomethionine-labelled crystals. Preliminary crystallographic analysis revealed that the crystals belonged to the hexagonal space groupP3112 (orP3212), with unit-cell parametersa=b= 88.9,c= 221.2 Å, α = 90, β = 90, γ = 120°, indicating that a dimer was present in the asymmetric unit.

scholarly journals Brattforsite, Mn19(AsO3)12Cl2, a new arsenite mineral related to magnussonite, from Brattforsgruvan, Nordmark, Värmland, Sweden

2021 ◽  
Author(s):  
Dan Holtstam ◽  
Cristian Biagioni ◽  
Ulf Hålenius
Keyword(s):  
Three Dimensional ◽  
Structural Data ◽  
Type Specimen ◽  
Structural Topology ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Calculated Density ◽  
X Ray ◽  
Cell Parameters ◽  
Density Values

AbstractBrattforsite is an approved mineral (IMA2019-127), with ideal formula Mn19(AsO3)12Cl2. Associated minerals in the type specimen from the Brattfors mine, Nordmark (Värmland, Sweden) include jacobsite, alleghanyite, phlogopite, calcite and dolomite. Brattforsite, forming subhedral, mostly equant crystals up to 0.5 mm across, is orange to reddish-brown with a white streak, and translucent with a resinous to vitreous lustre. The fracture is uneven to subconchoidal, and no cleavage is observed. It is very weakly pleochroic in yellow, optically biaxial (–) with 2V = 44(5)° and has calculated mean refractive index of 1.981. Measured and calculated density values are 4.49(1) and 4.54(1) g·cm− 3, respectively. Chemical analyses yields (in wt%): MgO 0.62, CaO 1.26, MnO 48.66, FeO 0.13, As2O3 46.72, Cl 2.61, H2Ocalc 0.07, O ≡ Cl –0.59, sum 99.49, corresponding to the empirical formula (Mn17.67Ca0.58Mg0.40Fe0.05)∑18.70As12.17O35.90Cl1.90(OH)0.20, based on 38 (O + Cl + OH) atoms per formula unit. The five strongest Bragg peaks in the powder X-ray diffraction pattern are [d (Å), I (%), (hkl)]: 2.843,100, ($$ \overline{4} $$ 4 - 44); 2.828, 99, (444); 1.731, 32, (880); 2.448, 28, (800); 1.739, 25, (088). Brattforsite is monoclinic and pseudotetragonal, space group I2/a, with unit-cell parameters a = 19.5806(7), b = 19.5763(7), c = 19.7595(7) Å, β = 90.393(3)°, V = 7573.9(5) Å3 and Z = 8. The crystal structure was solved and refined to an R1 index of 3.4 % for 7445 reflections [Fo > 4σ(Fo)]. Brattforsite has the same overall structural topology as magnussonite (i.e., the species can be considered as homeotypic), but with 12 independent tetrahedrally coordinated As sites and 21 Mn sites with varying (4–8) coordination. The Mn-centered polyhedra, bonded through edge- and face-sharing, give rise to a three-dimensional framework. The (AsO3)3− groups are bonded to this framework through corner- and edge-sharing. Spectroscopic measurements (optical absorption, Raman, FTIR) carried out support the interpretation of the compositional and structural data.

scholarly journals Crystallization and preliminary X-ray diffraction studies of the family 54 carbohydrate-binding module from laminarinase (β-1,3-glucanase) Lic16A ofClostridium thermocellum

2015 ◽  
Vol 71 (2) ◽  
pp. 217-220 ◽  
Author(s):  
Yury A. Kislitsyn ◽  
Valeriya R. Samygina ◽  
Igor A. Dvortsov ◽  
Nataliya A. Lunina ◽  
Inna P. Kuranova ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Diffusion Method ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Module ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
The Family ◽  
Overexpression System

The crystallization and preliminary X-ray diffraction analysis of the carbohydrate-binding module (CBM) from laminarinase Lic16A of the hyperthermophilic anaerobic bacteriumClostridium thermocellum(ctCBM54) are reported. Recombinant ctCBM54 was prepared using anEscherichia coli/pQE30 overexpression system and was crystallized by the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 2.1 Å resolution using synchrotron radiation. The crystals belonged to space groupP6322, with unit-cell parametersa=b= 130.15,c= 131.05 Å. The three-dimensional structure of ctCBM54 will provide valuable information about the structure–function relation of the laminarinase Lic16A and will allow the exploitation of this binding module in biotechnological applications.

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

2015 ◽  
Vol 71 (6) ◽  
pp. 676-679 ◽  
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.

scholarly journals Crystallization and preliminary X-ray diffraction data for a purple acid phosphatase from sweet potato

1999 ◽  
Vol 55 (12) ◽  
pp. 2051-2052 ◽  
Author(s):  
Gerhard Schenk ◽  
Lyle E. Carrington ◽  
Susan E. Hamilton ◽  
John de Jersey ◽  
Luke W. Guddat
Keyword(s):  
Acid Phosphatase ◽  
Sweet Potato ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Purple Acid Phosphatase ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
The Subject

Purple acid phosphatase from sweet potato is a homodimer of 110 kDa. Two forms of the enzyme have been characterized. One contains an Fe–Zn centre similar to that previously reported for red kidney bean purple acid phosphatase. Another isoform, the subject of this work, is the first confirmed example of an Fe–Mn-containing enzyme. Crystals of this protein have been grown from PEG 6000. They have unit-cell parameters a = b = 118.4, c = 287.4 Å and have the symmetry of space group P6522, with one dimer per asymmetric unit. Diffraction data collected using a conventional X-ray source from a cryocooled crystal extend to 2.90 Å resolution. The three-dimensional structure of the enzyme will provide insight into the coordination of this novel binuclear metal centre.

scholarly journals Crystallization and preliminary X-ray diffraction studies of mammalian purple acid phosphatase

1999 ◽  
Vol 55 (8) ◽  
pp. 1462-1464 ◽  
Author(s):  
Luke W. Guddat ◽  
Alan S. McAlpine ◽  
David Hume ◽  
John de Jersey ◽  
Susan Hamilton ◽  
...  
Keyword(s):  
Acid Phosphatase ◽  
Rational Design ◽  
Three Dimensional ◽  
Allantoic Fluid ◽  
Bone Diseases ◽  
Purple Acid Phosphatase ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters

The oxidized form of purple acid phosphatase from pig allantoic fluid has been crystallized in the presence of phosphate using the hanging-drop technique. The crystals belong to the space group P212121 and have unit-cell parameters a = 66.8, b = 70.3, c = 78.7 Å. Diffraction data collected from a cryocooled crystal using a conventional X-ray source extend to 1.55 Å resolution. A knowledge of the three-dimensional structure of mammalian purple acid phosphatase will aid in understanding the substrate specificity of the enzyme and will be important in the rational design of inhibitors, with potential in the treatment of bone diseases.

Three Dimensional Structure of UMo8O26: Ordering of U-Vacancies

2002 ◽  
Vol 718 ◽  
Author(s):  
N.D. Zakharov ◽  
P. Werner
Keyword(s):  
Low Temperatures ◽  
Driving Force ◽  
Three Dimensional ◽  
Solid State Reaction Method ◽  
Dimensional Structure ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Selected Area Electron Diffraction ◽  
Transmission Electron ◽  
Edx Microanalysis

AbstractThe structure and composition of UMo8O26 synthesized by solid state reaction method have been investigated by High Resolution Transmission Electron Microscopy (HRTEM), Selected Area Electron Diffraction, and EDX microanalysis. The ordering of U vacancies results in considerable enlargement of unit cell parameters: an=6.44 nm, bn=1.45 nm, cn=1.6 nm. It is build up of four layers piled up in c direction. Each following layer is shifted relative to previous one by vector bn/4. Eight hexagonal tunnels in each layer are filled by U atoms, while the eight others are vacant (V). Interaction between U cations and vacancies is driving force for ordering. The variation of stoichiometry can be a reason for appearance of incommensurate modulations in these crystals. It seems plausible that this structure might also exhibit superconductivity at low temperatures.

Structural Study of a new Compound Based on Acid 1,4-Cyclohexanedicarboxylic (1,4-CDC)

2010 ◽  
Vol 6 (1) ◽  
pp. 891-896
Author(s):  
Manel Halouani ◽  
M. Dammak ◽  
N. Audebrand ◽  
L. Ktari
Keyword(s):  
Aqueous Solution ◽  
Water Molecules ◽  
Carboxyl Group ◽  
X Ray Diffraction ◽  
Compound I ◽  
Unit Cell Parameters ◽  
Monoclinic System ◽  
X Ray ◽  
Cell Parameters ◽  
Cyclohexanedicarboxylic Acid

One nickel 1,4-cyclohexanedicarboxylate coordination polymers, Ni2 [(O10C6H4)(COO)2].2H2O  (I), was hydrothermally synthesized from an aqueous solution of Ni (NO3)2.6H2O, (1,4-CDC) (1,4-CDC = 1,4-cyclohexanedicarboxylic acid) and tetramethylammonium nitrate. Compound (I) crystallizes in the monoclinic system with the C2/m space group. The unit cell parameters are a = 20.1160 (16) Å, b = 9.9387 (10) Å, c = 6.3672 (6) Å, β = 97.007 (3) (°), V= 1263.5 (2) (Å3) and Dx= 1.751g/cm3. The refinement converged into R= 0.036 and RW = 0.092. The structure, determined by single crystal X-ray diffraction, consists of two nickel atoms Ni (1) and Ni (2). Lots of ways of which is surrounded by six oxygen atoms, a carboxyl group and two water molecules.

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