scholarly journals Crystallization and X-ray diffraction analysis of chondroitin lyase from baculovirus: envelope protein ODV-E66

2012 ◽  
Vol 68 (2) ◽  
pp. 190-192 ◽  
Author(s):  
Yoshirou Kawaguchi ◽  
Nobuo Sugiura ◽  
Momo Onishi ◽  
Koji Kimata ◽  
Makoto Kimura ◽  
...  
Keyword(s):  
Amino Acids ◽  
Diffraction Analysis ◽  
Envelope Protein ◽  
Unique Characteristic ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Baculovirus Infection

Baculovirus envelope protein ODV-E66 (67–704), in which the N-terminal 66 amino acids are truncated, is a chondroitin lyase. It digests chondroitin and chondroitin 6-sulfate efficiently, but does not digest chondroitin 4-sulfate. This unique characteristic is useful for the preparation of specific chondroitin oligosaccharides and for investigation of the mechanism of baculovirus infection. ODV-E66 (67–704) was crystallized; the crystal diffracted to 1.8 Å resolution and belonged to space groupP62orP64, with unit-cell parametersa = b = 113.5,c= 101.5 Å. One molecule is assumed to be present per asymmetric unit, which gives a Matthews coefficient of 2.54 Å3 Da−1.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of rat autotaxin

2010 ◽  
Vol 66 (9) ◽  
pp. 1127-1129 ◽  
Author(s):  
Jacqueline E. Day ◽  
Troii Hall ◽  
Lyle E. Pegg ◽  
Timothy E. Benson ◽  
Jens Hausmann ◽  
...  
Keyword(s):  
Diffraction Analysis ◽  
Sodium Thiocyanate ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
X Ray ◽  
Cell Parameters ◽  
Maximum Resolution

Rat autotaxin has been cloned, expressed, purified to homogeneity and crystallizedviahanging-drop vapour diffusion using PEG 3350 as precipitant and ammonium iodide and sodium thiocyanate as salts. The crystals diffracted to a maximum resolution of 2.05 Å and belonged to space groupP1, with unit-cell parametersa= 53.8,b= 63.3,c= 70.5 Å, α = 98.8, β = 106.2, γ = 99.8°. Preliminary X-ray diffraction analysis indicated the presence of one molecule per asymmetric unit, with a solvent content of 47%.

scholarly journals Crystallization and X-ray diffraction analysis of native and selenomethionine-substituted PhyH-DI fromBacillussp. HJB17

2017 ◽  
Vol 73 (11) ◽  
pp. 607-611
Author(s):  
Fang Lu ◽  
Bei Zhang ◽  
Yong Liu ◽  
Ying Song ◽  
Gangxing Guo ◽  
...  
Keyword(s):  
Unit Cell ◽  
Diffusion Method ◽  
Data Sets ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Phytases are phosphatases that hydrolyze phytates to less phosphorylatedmyo-inositol derivatives and inorganic phosphate. β-Propeller phytases, which are very diverse phytases with improved thermostability that are active at neutral and alkaline pH and have absolute substrate specificity, are ideal substitutes for other commercial phytases. PhyH-DI, a β-propeller phytase fromBacillussp. HJB17, was found to act synergistically with other single-domain phytases and can increase their efficiency in the hydrolysis of phytate. Crystals of native and selenomethionine-substituted PhyH-DI were obtained using the vapour-diffusion method in a condition consisting of 0.2 Msodium chloride, 0.1 MTris pH 8.5, 25%(w/v) PEG 3350 at 289 K. X-ray diffraction data were collected to 3.00 and 2.70 Å resolution, respectively, at 100 K. Native PhyH-DI crystals belonged to space groupC121, with unit-cell parametersa = 156.84,b = 45.54,c = 97.64 Å, α = 90.00, β = 125.86, γ = 90.00°. The asymmetric unit contained two molecules of PhyH-DI, with a corresponding Matthews coefficient of 2.17 Å3 Da−1and a solvent content of 43.26%. Crystals of selenomethionine-substituted PhyH-DI belonged to space groupC2221, with unit-cell parametersa = 94.71,b= 97.03,c= 69.16 Å, α = β = γ = 90.00°. The asymmetric unit contained one molecule of the protein, with a corresponding Matthews coefficient of 2.44 Å3 Da−1and a solvent content of 49.64%. Initial phases for PhyH-DI were obtained from SeMet SAD data sets. These data will be useful for further studies of the structure–function relationship of PhyH-DI.

scholarly journals Purification, crystallization and preliminary X-ray diffraction analysis of Imp3 in complex with an Mpp10 peptide involved in yeast ribosome biogenesis

2014 ◽  
Vol 70 (7) ◽  
pp. 918-921 ◽  
Author(s):  
Sanduo Zheng ◽  
Keqiong Ye
Keyword(s):  
Diffraction Analysis ◽  
Associated Factors ◽  
Ribosome Biogenesis ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Vast Number ◽  
X Ray ◽  
Cell Parameters ◽  
Early Processing ◽  
Ribosomal Particle

Eukaryotic ribosome synthesis requires a vast number of transiently associated factors. Mpp10, Imp3 and Imp4 form a protein complex in the 90S pre-ribosomal particle that conducts early processing of 18S rRNA. Here, a short fragment of Mpp10 was identified to associate with and increase the solubility of Imp3. An Imp3–Mpp10 complex was co-expressed, co-purified and co-crystallized. Preliminary X-ray diffraction analysis revealed that the crystal diffracted to 2.1 Å resolution and belonged to space groupP212121, with unit-cell parametersa= 51.6,b= 86.9,c= 88.7 Å.

Preparation and preliminary X-ray diffraction studies of a new crystal form of L-asparaginase from Escherichia coli

1999 ◽  
Vol 55 (9) ◽  
pp. 1616-1617
Author(s):  
I. Polikarpov ◽  
R. T. de Oliveira ◽  
J. Abrahão-Neto
Keyword(s):  
Escherichia Coli ◽  
Synchrotron Radiation ◽  
Crystal Form ◽  
Asymmetric Unit ◽  
Chemotherapeutic Drug ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Synchrotron Radiation Diffraction

L-Asparaginase is an enzyme which hydrolyzes asparagine to produce aspartic acid and ammonia. It is an effective chemotherapeutic drug, especially in the treatment of acute lymphoblastic leukaemia in children. The enzyme from Escherichia coli was crystallized in a new crystal form with space group C2, unit-cell parameters a = 76.3 (0), b = 134.6 (2), c = 64.8 (7) Å, β = 110.5 (1)° and a dimer in the asymmetric unit. Synchrotron-radiation diffraction data have been collected to 1.95 Å resolution.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of human DNA primase

2014 ◽  
Vol 70 (2) ◽  
pp. 206-210 ◽  
Author(s):  
Andrey G. Baranovskiy ◽  
Jianyou Gu ◽  
Nigar D. Babayeva ◽  
Vinod B. Agarkar ◽  
Yoshiaki Suwa ◽  
...  
Keyword(s):  
Active Site ◽  
Large Subunit ◽  
Structural Studies ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Human Dna ◽  
Structural Details

Human primase synthesizes RNA primers and transfers them to the active site of Pol α with subsequent extension with dNTPs. Human primase is a heterodimer of two subunits: a small catalytic subunit (p49) and a large subunit (p58). The structural details of the initiation and elongation steps of primer synthesis, as well as primer length counting, are not known. To address these questions, structural studies of human primase were initiated. Two types of crystals were obtained. The best diffracting crystals belonged to space groupP1, with unit-cell parametersa= 86.2,b= 88.9,c= 94.68 Å, α = 93.82, β = 96.57, γ = 111.72°, and contained two heterodimers of full-length p49 and p59 subunits in the asymmetric unit.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of Trap1 complexed with Hsp90 inhibitors

2014 ◽  
Vol 70 (12) ◽  
pp. 1683-1687 ◽  
Author(s):  
Hanbin Jeong ◽  
Byoung Heon Kang ◽  
Changwook Lee
Keyword(s):  
Diffraction Analysis ◽  
Diffusion Method ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Hsp90 Inhibitors ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Middle Domain ◽  
Client Proteins

Hsp90 is a molecular chaperone responsible for the assembly and regulation of many cellular client proteins. In particular, Trap1, a mitochondrial Hsp90 homologue, plays a pivotal role in maintaining mitochondrial integrity, protecting against apoptosis in cancer cells. The N (N-terminal)-M (middle) domain of human Trap1 was crystallized in complex with Hsp90 inhibitors (PU-H71 and BIIB-021) by the hanging-drop vapour-diffusion method at pH 6.5 and 293 K using 15% PEG 8K as a precipitant. Diffraction data were collected from crystals of the Trap1–PU-H71 (2.7 Å) and Trap1–BIIB-021 (3.1 Å) complexes to high resolution at a synchrotron-radiation source. Preliminary X-ray diffraction analysis revealed that both crystals belonged to space groupP41212 orP43212, with unit-cell parametersa=b= 69.2,c= 252.5 Å, and contained one molecule per asymmetric unit according to Matthews coefficient calculations.

scholarly journals Preliminary X-ray crystallographic studies of the TIR domain of human Toll-like receptor 6

2014 ◽  
Vol 70 (8) ◽  
pp. 1053-1055 ◽  
Author(s):  
Tae-ho Jang ◽  
Hyun Ho Park
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Immune Response ◽  
Innate Immune ◽  
Toll Like Receptor ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Tir Domain

Toll-like receptor (TLR) proteins have been identified and shown to play a role in the innate immune response. TLR6 associated with TLR2 can recognize diacylated lipoprotein. In this study, the human TLR6 TIR domain corresponding to amino acids 640–796 was overexpressed inEscherichia coliusing engineered C-terminal His tags. The TLR6 TIR domain was then purified to homogeneity and crystallized at 20°C. Finally, X-ray diffraction data were collected to a resolution of 2.2 Å from a crystal belonging to space groupC2, with unit-cell parametersa= 127.60,b= 44.20,c= 75.72 Å, β = 118.89°

scholarly journals Overproduction, crystallization and preliminary X-ray crystallographic analysis ofEscherichia colitRNAN6-threonylcarbamoyladenosine dehydratase

2014 ◽  
Vol 70 (11) ◽  
pp. 1517-1520 ◽  
Author(s):  
Sunmin Kim ◽  
Keon Young Kim ◽  
Jeong Kuk Park ◽  
Byung Il Lee ◽  
Yun-Gon Kim ◽  
...  
Keyword(s):  
Crystallographic Analysis ◽  
X Rays ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
E Coli ◽  
Protein Mass ◽  
Crystal Volume

Escherichia colitRNAN6-threonylcarbamoyladenosine dehydratase (TcdA), previously called CsdL or YgdL, was overproduced and purified fromE. coliand crystallized using polyethylene glycol 3350 as a crystallizing agent. X-ray diffraction data were collected to 2.70 Å resolution under cryoconditions using synchrotron X-rays. The crystals belonged to space groupP21, with unit-cell parametersa= 65.4,b= 96.8,c= 83.3 Å, β = 111.7°. According to the Matthews coefficient, the asymmetric unit may contain up to four subunits of the monomeric protein, with a crystal volume per protein mass (VM) of 2.12 Å3 Da−1and 42.1% solvent content.

scholarly journals Recombinant expression, purification, crystallization and preliminary X-ray diffraction analysis ofHaemophilus influenzaeBamD and BamCD complex

2015 ◽  
Vol 71 (2) ◽  
pp. 234-238
Author(s):  
Jintang Lei ◽  
Xun Cai ◽  
Xiaodan Ma ◽  
Li Zhang ◽  
Yuwen Li ◽  
...  
Keyword(s):  
Diffraction Analysis ◽  
Recombinant Expression ◽  
Outer Membrane Proteins ◽  
Gel Filtration ◽  
Unit Cell ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

The Bam machinery, which is highly conserved from bacteria to humans, is well recognized as the apparatus responsible for the insertion and folding of most outer membrane proteins in Gram-negative bacteria. InEscherichia coli, the Bam machinery consists of five components (i.e.BamA, BamB, BamC, BamD and BamE). In comparison, there are only four partners inHaemophilus influenzae: a BamB homologue is not found in its genome. In this study, the recombinant expression, purification, crystallization and preliminary X-ray diffraction analysis ofH. influenzaeBamD and BamCD complex are reported. The genes encoding BamC and BamD were cloned into a pET vector and expressed inE. coli. Affinity, ion-exchange and gel-filtration chromatography were used to obtain high-purity protein for further crystallographic characterization. Using the hanging-drop vapour-diffusion technique, BamD and BamCD protein crystals of suitable size were obtained using protein concentrations of 70 and 50 mg ml−1, respectively. Preliminary X-ray diffraction analysis showed that the BamD crystals diffracted to 4.0 Å resolution and belonged to space groupP212121, with unit-cell parametersa= 54.5,b= 130.5,c= 154.7 Å. The BamCD crystals diffracted to 3.8 Å resolution and belonged to space groupI212121, with unit-cell parametersa= 101.6,b= 114.1,c= 234.9 Å.

Crystal chemistry and nomenclature of fillowite-type phosphates

2021 ◽  
Vol 59 (4) ◽  
pp. 781-796
Author(s):  
Frédéric Hatert ◽  
Edward S. Grew ◽  
Pietro Vignola ◽  
Nicola Rotiroti ◽  
Fabrizio Nestola ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Divalent Cations ◽  
Complex Structure ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Cation Sites ◽  
Cation Distributions

ABSTRACT The crystal chemistries of five samples of minerals belonging to the fillowite group were structurally investigated: (A) fillowite from the Buranga pegmatite, Rwanda; (B) fillowite from the Kabira pegmatite, Uganda; (C) johnsomervilleite from Loch Quoich, Scotland; (D) johnsomervilleite from the Malpensata pegmatite, Italy; and (E) chladniite from the Sapucaia pegmatite, Minas Gerais, Brazil. Their crystal structures were refined in space group R (No. 148), using single-crystal X-ray diffraction data, to R1 values of (A) 3.79%, (B) 3.52%, (C) 4.14%, (D) 4.04%, and (E) 5.59%. Unit-cell parameters are: (A) a = 15.122(1), c = 43.258(4) Å; (B) a = 15.125(1), c = 43.198(3) Å; (C) a = 15.036(2), c = 42.972(9) Å; (D) a = 15.090(2), c = 43.050(9) Å; and (E) a = 15.1416(6), c = 43.123(2) Å. The asymmetric unit contains 15 cation sites with coordinations ranging from V to IX, as well as six P sites. The complex structure can be split into three types of chains running parallel to the c axis. These chains are composed of edge- and face-sharing polyhedra. Detailed cation distributions were determined for all five samples, and their comparison allowed us to establish the general formula A3BC11(PO4)9 for fillowite-type phosphates, where A represents the group of sites mainly occupied by Na, B the Ca sites, and C the sites containing the divalent cations Fe2+, Mn, and Mg. This formula was accepted by the CNMNC, and the four valid mineral species occurring in the fillowite group are fillowite (C = Mn), johnsomervilleite (C = Fe2+), chladniite (C = Mg), and galileiite (B and C = Fe2+). Stornesite-(Y) is discredited, since this mineral corresponds to Y-bearing chladniite.

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