Crystallization and preliminary X-ray diffraction studies on the conserved GTPase domain of the signal recognition particle from Acidianus ambivalens

1999 ◽  
Vol 55 (11) ◽  
pp. 1949-1951 ◽  
Author(s):  
Guillermo Montoya ◽  
Kai te Kaat ◽  
Ralf Moll ◽  
Günter Schäfer ◽  
Irmgard Sinning
Keyword(s):  
Signal Recognition Particle ◽  
Signal Recognition ◽  
Resolution Limit ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
Data Set ◽  
X Ray ◽  
Cell Parameters ◽  
Ras Gtpases ◽  
Crystallization Experiments

The signal recognition particle (SRP) of bacteria consists of only one protein, known as Ffh or the SRP54 homologue, which forms a complex with 4.5S RNA. It also binds to signal peptides and contains a GTPase which displays interesting differences to Ras GTPases. The conserved NG-domain of Ffh from the archaebacterium Acidianus ambivalens was cloned and overexpressed with a C-terminal His tag in Escherichia coli. Crystallization experiments of the native protein as well as of the Thr112Ala mutant, which is deficient in GTP hydrolysis, resulted in crystals suitable for X-ray diffraction. The crystals belong to the orthorhombic space group C2221, with unit-cell parameters a = 64.5, b = 128.3, c = 72.0 Å. At cryogenic temperatures, the crystals diffracted to a resolution limit of 2.8 Å using a rotating-anode generator and contain one molecule per asymmetric unit. A native data set has been collected using synchrotron radiation to around 2.0 Å resolution. Selenomethionine protein was produced; its crystals diffract in-house to about 2.8 Å resolution.

scholarly journals Expression, purification, crystallization and preliminary X-ray diffraction analysis of the dihydroorotase domain of human CAD

2012 ◽  
Vol 68 (11) ◽  
pp. 1341-1345 ◽  
Author(s):  
Nada Lallous ◽  
Araceli Grande-García ◽  
Rafael Molina ◽  
Santiago Ramón-Maiques
Keyword(s):  
De Novo ◽  
Structural Information ◽  
Protein Molecule ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
Data Set ◽  
X Ray ◽  
Cell Parameters ◽  
Small Crystals ◽  
Crystallization Experiments

CAD is a 243 kDa eukaryotic multifunctional polypeptide that catalyzes the first three reactions ofde novopyrimidine biosynthesis: glutamine-dependentcarbamyl phosphate synthetase,aspartate transcarbamylase anddihydroorotase (DHO). In prokaryotes, these activities are associated with monofunctional proteins, for which crystal structures are available. However, there is no detailed structural information on the full-length CAD protein or any of its functional domains apart from that it associates to form a homohexamer of ∼1.5 MDa. Here, the expression, purification and crystallization of the DHO domain of human CAD are reported. The DHO domain forms homodimers in solution. Crystallization experiments yielded small crystals that were suitable for X-ray diffraction studies. A diffraction data set was collected to 1.75 Å resolution using synchrotron radiation at the SLS, Villigen, Switzerland. The crystals belonged to the orthorhombic space groupC2221, with unit-cell parametersa= 82.1,b= 159.3,c= 61.5 Å. The Matthews coefficient calculation suggested the presence of one protein molecule per asymmetric unit, with a solvent content of 48%.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of the homing endonuclease I-CvuI fromChlorella vulgarisin complex with its target DNA

2014 ◽  
Vol 70 (2) ◽  
pp. 256-259 ◽  
Author(s):  
Pilar Redondo ◽  
Nekane Merino ◽  
Maider Villate ◽  
Francisco J. Blanco ◽  
Guillermo Montoya ◽  
...  
Keyword(s):  
Diffraction Analysis ◽  
Homing Endonuclease ◽  
Homing Endonucleases ◽  
Resolution Limit ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
Strand Breaks ◽  
X Ray ◽  
Cell Parameters ◽  
Wide Range

Homing endonucleases are highly specific DNA-cleaving enzymes that recognize long stretches of DNA. The engineering of these enzymes provides novel instruments for genome modification in a wide range of fields, including gene targeting, by inducing specific double-strand breaks. I-CvuI is a homing endonuclease from the green algaChlorella vulgaris. This enzyme was purified after overexpression inEscherichia coli. Crystallization experiments of I-CvuI in complex with its DNA target in the presence of Mg2+yielded crystals suitable for X-ray diffraction analysis. The crystals belonged to the orthorhombic space groupP212121, with unit-cell parametersa= 62.83,b= 83.56,c= 94.40 Å. The self-rotation function and the Matthews coefficient suggested the presence of one protein–DNA complex per asymmetric unit. The crystals diffracted to a resolution limit of 1.9 Å using synchrotron radiation.

scholarly journals Purification, crystallization and preliminary X-ray diffraction analysis of a soluble variant of the monoglyceride lipase Yju3p from the yeastSaccharomyces cerevisiae

2015 ◽  
Vol 71 (2) ◽  
pp. 243-246 ◽  
Author(s):  
Srinivasan Rengachari ◽  
Philipp Aschauer ◽  
Christian Sturm ◽  
Monika Oberer
Keyword(s):  
Crystal Form ◽  
Size Exclusion ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
Data Set ◽  
X Ray ◽  
Cell Parameters ◽  
Monoglyceride Lipase ◽  
Exclusion Chromatography

The protein Yju3p is the orthologue of monoglyceride lipases in the yeastSaccharomyces cerevisiae. A soluble variant of this lipase termed s-Yju3p (38.3 kDa) was generated and purified to homogeneity by affinity and size-exclusion chromatography. s-Yju3p was crystallized in a vapour-diffusion setup at 293 K and a complete data set was collected to 2.4 Å resolution. The crystal form was orthorhombic (space groupP212121), with unit-cell parametersa= 77.2,b= 108.6,c= 167.7 Å. The asymmetric unit contained four molecules with a solvent content of 46.4%.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of UspE fromEscherichia coli

2014 ◽  
Vol 70 (12) ◽  
pp. 1640-1642 ◽  
Author(s):  
Yongbin Xu ◽  
Chun-Shan Quan ◽  
Xuanzhen Jin ◽  
Xiaoling Jin ◽  
Jing Zhao ◽  
...  
Keyword(s):  
Stress Proteins ◽  
Gel Filtration ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Data Set ◽  
X Ray ◽  
Cell Parameters ◽  
E Coli ◽  
Vapour Diffusion ◽  
Induced Genes

Universal stress proteins (Usps) are among the most highly induced genes when bacteria are subjected to several stress conditions such as heat shock, nutrient starvation or the presence of oxidants or other stress agents.Escherichia colihas five small Usps and one tandem-type Usp. UspE (or YdaA) is the tandem-type Usp and consists of two Usp domains arranged in tandem. To date, the structure of UspE remains to be elucidated. To contribute to the molecular understanding of the function of the tandem-type UspE, UspE fromE. coliwas overexpressed and the recombinant protein was purified using Ni–NTA affinity, Q anion-exchange and gel-filtration chromatography. Crystals of UspE were obtained by sitting-drop vapour diffusion. A diffraction data set was collected to a resolution of 3.2 Å from flash-cooled crystals. The crystals belonged to the tetragonal space groupI4122 orI4322, with unit-cell parametersa=b= 121.1,c = 241.7 Å.

scholarly journals Crystallization, optimization and preliminary X-ray characterization of a metal-dependent PI-PLC fromStreptomyces antibioticus

2012 ◽  
Vol 68 (11) ◽  
pp. 1378-1386 ◽  
Author(s):  
Michael R. Jackson ◽  
Thomas L. Selby
Keyword(s):  
X Ray Diffraction ◽  
Hanging Drop ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Streptomyces Antibioticus ◽  
Cell Parameters ◽  
Heavy Atoms ◽  
Hanging Drop Method

A recombinant metal-dependent phosphatidylinositol-specific phospholipase C (PI-PLC) fromStreptomyces antibioticushas been crystallized by the hanging-drop method with and without heavy metals. The native crystals belonged to the orthorhombic space groupP222, with unit-cell parametersa= 41.26,b= 51.86,c = 154.78 Å. The X-ray diffraction results showed significant differences in the crystal quality of samples soaked with heavy atoms. Additionally, drop pinning, which increases the surface area of the drops, was also used to improve crystal growth and quality. The combination of heavy-metal soaks and drop pinning was found to be critical for producing high-quality crystals that diffracted to 1.23 Å resolution.

Determination of the Crystal Structure and Redefinition of Tsugaruite, Pb28As15S50Cl, the First Lead-Arsenic Chloro-Sulfosalt

2020 ◽  
Author(s):  
Cristian Biagioni ◽  
Luca Bindi ◽  
Koichi Momma ◽  
Ritsuro Miyawaki ◽  
Yoshitaka Matsushita ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Atomic Ratio ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Specific Position ◽  
Actual Classification ◽  
Aomori Prefecture

Abstract Tsugaruite was originally defined as a lead-arsenic sulfosalt from the Yunosawa mine, Aomori Prefecture, Japan. Until recently its crystal structure remained unsolved and its actual classification in the sulfosalt realm was unknown. Here the refinement of the crystal structure of tsugaruite using single-crystal X-ray diffraction data is reported. The mineral is orthorhombic, space group P2nn, with unit-cell parameters a = 8.0774(10), b = 15.1772(16), c = 38.129(4) Å, V = 4674.3(9) Å3, in agreement with previous studies. The solution of the crystal structure of this mineral revealed Cl occupying a specific position. Chlorine was thus sought and found using the electron microprobe; the average of six spot analyses gave (in wt.%): Pb 68.04, As 12.83, S 18.29, Cl 0.63, total 99.80. The empirical formula, calculated on the basis of Pb + As = 43 atoms per formula unit, is Pb28.26As14.74S49.08Cl1.52. Tsugaruite is an N = 4 plesiotypic derivative of the homologous series of Pb-Sb chloro-sulfosalts having the general formula Pb(2+2N)(Sb,Pb)(2+2N)S(2+2N)(S,Cl)(4+2N)ClN. It has a Cl/(Cl + S) atomic ratio close to that of other known Pb-Sb chloro-sulfosalts (pillaite, pellouxite) and slightly higher than that of dadsonite.

Crystal Structures and Stability of Two Bipyridyl Complexes of Metal Chloroacetates

2007 ◽  
Vol 62 (10) ◽  
pp. 1271-1276 ◽  
Author(s):  
Liang Chen ◽  
Xian-Wen Wanga ◽  
Jing-Zhong Chen ◽  
Jian-Hong Liu
Keyword(s):  
Binuclear Complexes ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
Reaction Conditions ◽  
Triclinic Space Group ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Dimensional Network

The complexes Mn(Cl3CCOO)2(4,4′-bpy) (1) and [Cu2(ClCH2COO)(2,2′-bpy)2(OH)(H2O)]-(NO3)2(2) (bpy = bipyridine) were generated under mild reaction conditions and characterized by IR spectra, thermogravimetric analysis (TGA), X-ray powder diffraction (XRD), and single crystal X-ray diffraction. Compound 1 exhibits a two-dimensional network with octahedrally coordinated Mn(II) atoms linked by 4,4′-bpy ligands and Cl3COO− ligands. Compound 2 features a supramolecular structure of binuclear complexes, with edge-sharing five-coordinated square-pyramidal units bridged by the ClCH2COO− ligand, an OH− group and a water molecule. Complex 1 crystallizes in the orthorhombic space group Pbcn with cell parameters: a = 16.5390(17), b = 11.6396(17), c = 9.9181(12) Å, V = 1909.3(4) Å3, Z = 4, wR2 = 0.1576. Complex 2 crystallizes in the triclinic space group P1̅ with cell parameters: a = 7.6190(15), b = 11.151(2), c = 16.640(3) Å , α = 73.13(3), β = 80.89(3), γ = 74.51(3)°, V = 1298.73(4) Å3, Z = 2, wR2 = 0.1265.

scholarly journals Purification, crystallization and preliminary crystallographic analysis of a 4-thiouridine synthetase–RNA complex

2013 ◽  
Vol 69 (4) ◽  
pp. 421-424 ◽  
Author(s):  
Peter-Thomas Naumann ◽  
Charles T. Lauhon ◽  
Ralf Ficner
Keyword(s):  
Diffraction Data ◽  
Thermotoga Maritima ◽  
Crystallographic Analysis ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Dependent Modification ◽  
Rna Complex

The sulfurtransferase 4-thiouridine synthetase (ThiI) is involved in the ATP-dependent modification of U8 in tRNA. ThiI fromThermotoga maritimawas cloned, overexpressed and purified. A complex comprising ThiI and a truncated tRNA was prepared and crystallized, and X-ray diffraction data were collected to a resolution of 3.5 Å. The crystals belonged to the orthorhombic space groupP212121, with unit-cell parametersa= 102.9,b= 112.8,c= 132.8 Å.

Crystallization and improvement of crystal quality for X-ray diffraction of maltooligosyl trehalose synthase by reductive methylation of lysine residues

1999 ◽  
Vol 55 (4) ◽  
pp. 931-933 ◽  
Author(s):  
Masanori Kobayashi ◽  
Michio Kubota ◽  
Yoshiki Matsuura
Keyword(s):  
Crystal Quality ◽  
X Ray Diffraction ◽  
Reductive Methylation ◽  
Orthorhombic Space Group ◽  
Trehalose Synthase ◽  
X Ray ◽  
Cell Parameters ◽  
Lysine Residues ◽  
Trehalose Biosynthesis ◽  
Enzyme Molecules

Maltooligosyl trehalose synthase, one of the two enzymes in the coupled trehalose biosynthesis system in Sulfolobus acidocaldarius, has been purified and crystallized. The chemical modification of this enzyme by reductive methylation of lysine residues significantly improved the crystal quality for X-ray diffraction experiments. The crystals of the modified enzyme belong to orthorhombic space group P212121, with unit-cell parameters a = 56.70, b = 140.1, c = 205.2 Å measured at cryo-temperature, and are found to contain two enzyme molecules per asymmetric unit.

scholarly journals Expression, purification, crystallization and preliminary X-ray crystallographic analysis of Enpp6

2014 ◽  
Vol 70 (6) ◽  
pp. 794-799 ◽  
Author(s):  
Junko Morita ◽  
Kazuki Kato ◽  
Emiko Mihara ◽  
Ryuichiro Ishitani ◽  
Junichi Takagi ◽  
...  
Keyword(s):  
Catalytic Domain ◽  
Crystallographic Analysis ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Data Set ◽  
X Ray ◽  
Cell Parameters ◽  
Choline Metabolism ◽  
Protein Molecules ◽  
Membrane Bound

Enpp (ectonucleotide phosphodiesterase/pyrophosphatase) 6 is a membrane-bound glycoprotein that hydrolyzes choline-containing compounds such as lysophosphatidylcholine and glycerophosphorylcholine, and presumably participates in choline metabolism. The catalytic domain of mouse Enpp6 was expressed in HEK293T cells, purified using the TARGET tag/P20.1-Sepharose system and crystallized. An X-ray diffraction data set was collected to 1.8 Å resolution. The crystal belonged to space groupP1, with unit-cell parametersa= 63.7,b= 68.8,c= 69.7 Å, α = 60.6, β = 87.0, γ = 68.1°. Assuming the presence of two protein molecules per asymmetric unit, the solvent content was estimated to be 49.5%.

Sign in / Sign up

Export Citation Format

Share Document