scholarly journals Expression, purification, crystallization and crystallographic study of theAspergillus terreusaromatic prenyltransferase AtaPT

2015 ◽  
Vol 71 (7) ◽  
pp. 889-894 ◽  
Author(s):  
Bingquan Gao ◽  
Ridao Chen ◽  
Xiao Liu ◽  
Jungui Dai ◽  
Fei Sun
Keyword(s):  
Aromatic Compounds ◽  
Aspergillus Terreus ◽  
Biological Properties ◽  
Chemical Diversity ◽  
The Self ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Crystallographic Study ◽  
Rotation Function

Prenylated aromatics are produced by aromatic prenyltransferases during the secondary metabolism of bacteria, fungi and plants. The prenylation of nonprenylated precursors can lead to great chemical diversity and extensive biological properties.Aspergillus terreusaromatic prenyltransferase (AtaPT), which has recently been discovered and characterized, is such an enzyme and is responsible for the prenylation of various aromatic compounds. Here, recombinant AtaPT was overexpressed inEscherichia coli, purified and crystallized. Diffraction data were collected to a resolution of 1.71 Å and the crystal belonged to space groupP21212, with unit-cell parametersa= 96.2,b = 135.8,c= 69.5 Å, α = β = γ = 90°. Analysis of the calculated Matthews coefficient and the self-rotation function suggested that there are two AtaPT molecules in the asymmetric unit.

scholarly journals Neutron crystallographic study of heterotrimeric glutamine amidotransferase CAB

2019 ◽  
Vol 75 (3) ◽  
pp. 193-196
Author(s):  
Long Li ◽  
Motoyasu Adachi ◽  
Jian Yu ◽  
Koji Kato ◽  
Akira Shinoda ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Diffraction Data ◽  
Active Sites ◽  
Neutron Diffraction Data ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Crystallographic Study ◽  
Glutamine Amidotransferase

Heterotrimeric glutamine amidotransferase CAB (GatCAB) possesses an ammonia-self-sufficient mechanism in which ammonia is produced and used in the inner complex by GatA and GatB, respectively. The X-ray structure of GatCAB revealed that the two identified active sites of GatA and GatB are markedly distant, but are connected in the complex by a channel of 30 Å in length. In order to clarify whether ammonia is transferred through this channel in GatCAB by visualizing ammonia, neutron diffraction studies are indispensable. Here, GatCAB crystals were grown to approximate dimensions of 2.8 × 0.8 × 0.8 mm (a volume of 1.8 mm3) with the aid of a polymer using microseeding and macroseeding processes. Monochromatic neutron diffraction data were collected using the neutron single-crystal diffractometer BIODIFF at the Heinz Maier-Leibnitz Zentrum, Germany. The GatCAB crystals belonged to space group P212121, with unit-cell parameters a = 74.6, b = 94.5, c = 182.5 Å and with one GatCAB complex (molecular mass 119 kDa) in the asymmetric unit. This study represented a challenge in current neutron diffraction technology.

Crystallization and preliminary crystallographic study of HIP/PAP, a human C-lectin overexpressed in primary liver cancers

1999 ◽  
Vol 55 (8) ◽  
pp. 1487-1489 ◽  
Author(s):  
Chantal Abergel ◽  
Sabine Chenivesse ◽  
Marie-Georges Stinnakre ◽  
Sophie Guasco ◽  
Christian Bréchot ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Molecular Replacement ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
Adhesion Protein ◽  
Cell Parameters ◽  
Crystallographic Study ◽  
Liver Cancers ◽  
Replacement Solution

Human HIP/PAP is an adhesion protein expressed in normal pancreatic and Paneth cells and overexpressed in hepatocellular carcinoma. HIP/PAP was crystallized using the Hampton Research Crystal Screen and SAmBA software to define the optimal crystallization protocol. The crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 30.73, b = 49.35, c = 92.15 Å and one molecule in the asymmetric unit. Flash-frozen crystals diffract to 1.78 Å resolution using synchrotron radiation. A molecular-replacement solution was obtained using the human Reg/lithostathine structure and the AMoRe software.

scholarly journals Crystallographic analysis of FAD-dependent glucose dehydrogenase

2015 ◽  
Vol 71 (8) ◽  
pp. 1017-1019 ◽  
Author(s):  
Hirofumi Komori ◽  
Koji Inaka ◽  
Naoki Furubayashi ◽  
Michinari Honda ◽  
Yoshiki Higuchi
Keyword(s):  
Aspergillus Terreus ◽  
Glucose Dehydrogenase ◽  
Crystallographic Analysis ◽  
Diffusion Method ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Data Set ◽  
Solvent Content ◽  
X Ray ◽  
Cell Parameters

An FAD-dependent glucose dehydrogenase (GDH) fromAspergillus terreuswas purified and crystallized at 293 K using the sitting-drop vapour-diffusion method. A data set was collected to a resolution of 1.6 Å from a single crystal at 100 K using a rotating-anode X-ray source. The crystal belonged to space groupP21, with unit-cell parametersa= 56.56,b= 135.74,c= 74.13 Å, β = 90.37°. The asymmetric unit contained two molecules of GDH. The Matthews coefficient was calculated to be 2.2 Å3 Da−1and the solvent content was estimated to be 44%.

Crystallization and preliminary crystallographic study of triple-helical DNA

2000 ◽  
Vol 56 (1) ◽  
pp. 104-105 ◽  
Author(s):  
Zong-Jin Han ◽  
Sangkee Rhee ◽  
Keliang Liu ◽  
H. Todd Miles ◽  
David R. Davies
Keyword(s):  
Single Crystals ◽  
Unit Cell ◽  
The Other ◽  
Diffusion Method ◽  
Triplex Dna ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Crystallographic Study

Single crystals of d(CTCCTSCCGCGCG)·d(CGCGCGGAG) have been grown by the vapor-diffusion method using 2-methyl-2,4-pentanediol as a precipitant. The crystals are tetragonal, space group P42, with unit-cell parameters a = b = 53.8, c = 43.1 Å, and diffract to 1.8 Å resolution at a synchrotron X-ray beamline. In the crystal, the asymmetric unit contains one copy of the construct. The two halves of the structure are related by non-crystallographic twofold symmetry. These observations are consistent with the conclusion that the sequences of the 12-mer and 9-mer oligonucleotides form a duplex DNA at one end and a triplex DNA at the other end.

scholarly journals Crystallization and preliminary crystallographic study of human coronavirus NL63 main protease in complex with an inhibitor

2014 ◽  
Vol 70 (8) ◽  
pp. 1068-1071 ◽  
Author(s):  
Fenghua Wang ◽  
Yusheng Tan ◽  
Huiyan Li ◽  
Xia Chen ◽  
Jinshan Wang ◽  
...  
Keyword(s):  
Antiviral Drug ◽  
Proteolytic Processing ◽  
Genome Replication ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Human Coronavirus ◽  
Cell Parameters ◽  
Crystallographic Study ◽  
Main Protease ◽  
Complex Crystals

Human coronavirus NL63 mainly infects younger children and causes cough, fever, rhinorrhoea, bronchiolitis and croup. It encodes two polyprotein precursors required for genome replication and transcription. Each polyprotein undergoes extensive proteolytic processing, resulting in functional subunits. This process is mainly mediated by its genome-encoded main protease, which is an attractive target for antiviral drug design. In this study, the main protease of human coronavirus NL63 was crystallized in complex with a Michael acceptor. The complex crystals diffracted to 2.85 Å resolution and belonged to space groupP41212, with unit-cell parametersa=b= 87.2,c= 212.1 Å. Two molecules were identified per asymmetric unit.

scholarly journals Crystallographic analysis of RsmA, a ribosomal RNA small subunit methyltransferase A fromStaphylococcus aureus

2015 ◽  
Vol 71 (8) ◽  
pp. 1063-1066 ◽  
Author(s):  
Yang Liu ◽  
Yuwei Zhu ◽  
Maikun Teng ◽  
Xu Li
Keyword(s):  
Staphylococcus Aureus ◽  
Ribosomal Rna ◽  
Small Subunit ◽  
Crystallographic Analysis ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Rotation Function

RsmA, a ribosomal RNA small subunit methyltransferase fromStaphylococcus aureus, catalyzes theN6methylation of adenine in 16S rRNA. In this study, RsmA fromStaphylococcus aureuswas cloned, expressed, purified and crystallized. The crystal belonged to space groupC2, with unit-cell parametersa= 84.38,b= 157.76,c= 96.50 Å, β = 95.04°. X-ray diffraction data were collected to a resolution of 3.2 Å. The self-rotation function and the Matthews coefficient suggested the presence of two molecules in the asymmetric unit.

A Crystallographic Study of Bis[S-benzyl-5-bromo-2-oxoindolin-3-ylidenemethanehydrazonthioate] Disulfide Solvated with Dimethylsulfoxide

2012 ◽  
Vol 9 (2) ◽  
pp. 87
Author(s):  
Mohd Abdul Fatah Abdul Manan ◽  
M. Ibrahim M. Tahir ◽  
Karen A. Crouse ◽  
Fiona N.-F. How ◽  
David J. Watkin
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Solvent Molecule ◽  
Site Occupancy ◽  
Unit Cell Parameters ◽  
Intermolecular Hydrogen Bonds ◽  
Triclinic Space Group ◽  
Cell Parameters ◽  
Crystallographic Study ◽  
Thiol Form

The crystal structure of the title compound has been determined. The compound crystallized in the triclinic space group P -1, Z = 2, V = 1839 .42( 18) A3 and unit cell parameters a= 11. 0460( 6) A, b = 13 .3180(7) A, c=13. 7321 (8) A, a = 80.659(3 )0, b = 69 .800(3 )0 and g = 77 .007 (2)0 with one disordered dimethylsulfoxide solvent molecule with the sulfur and oxygen atoms are distributed over two sites; S101/S102 [site occupancy factors: 0.6035/0.3965] and 0130/0131 [site occupancy factor 0.3965/0.6035]. The C22-S2 l and C 19-S20 bond distances of 1. 779(7) A and 1. 788(8) A indicate that both of the molecules are connected by the disulfide bond [S20-S21 2.055(2) A] in its thiol form. The crystal structure reveals that both of the 5-bromoisatin moieties are trans with respect to the [S21-S20 and CI 9-Nl 8] and [S20-S21 and C22-N23] bonds whereas the benzyl group from the dithiocarbazate are in the cis configuration with respect to [S21-S20 and C19-S44] and [S20-S21 and C22-S36] bonds. The crystal structure is further stabilized by intermolecular hydrogen bonds of N9-H35···O16 formed between the two molecules and N28-H281 ···O130, N28-H281 ···O131 and C4 l-H4 l l ···O 131 with the solvent molecule.

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.

X-ray analysis of crystals of rat phosphatidylinositol-transfer protein with bound phosphatidylcholine

1999 ◽  
Vol 55 (2) ◽  
pp. 522-524 ◽  
Author(s):  
Randall L. Oliver ◽  
Jacqueline M. Tremblay ◽  
George M. Helmkamp ◽  
Lynwood R. Yarbrough ◽  
Natalie W. Breakfield ◽  
...  
Keyword(s):  
Crystal Form ◽  
Unit Cell ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Vapor Diffusion ◽  
Solvent Content ◽  
Cell Parameters ◽  
Transfer Protein ◽  
Phosphatidylinositol Transfer Protein ◽  
Phosphatidylinositol Transfer

Phosphatidylinositol-transfer protein (PITP) is a soluble, ubiquitously expressed, highly conserved protein encoded by two genes in humans, rodents and other mammals. A cDNA encoding the alpha isoform of the rat gene was expressed to high levels in Escherichia coli, the protein purified and the homogeneous protein used for crystallization studies. Crystals of rat PITP-α were obtained by vapor-diffusion techniques using the sitting-drop method. Crystals grow within two weeks by vapor-diffusion techniques in the presence of polyethylene glycol 4000. Both crystal forms pack in the monoclinic space group P21. Crystal form I has unit-cell parameters a = 44.75, b = 74.25, c = 48.32 Å and β = 114.14°. Unit-cell parameters for crystal form II are a = 47.86, b = 73.59, c = 80.49 Å and β = 98.54°. Crystal form I has a Vm of 2.295 Å3 Da−1 and an estimated solvent content of 46.4% with one molecule per asymmetric unit, while crystal form II has a Vm of 2.196 Å3 Da−1 and an estimated solvent content of 44.0%, assuming two molecules per asymmetric unit.

Synchrotron powder diffraction characterization of the zeolite-based (p-N,N-dimethylnitroaniline–mordenite) guest–host phase

2008 ◽  
Vol 64 (6) ◽  
pp. 713-724 ◽  
Author(s):  
Florence Porcher ◽  
Elena Borissenko ◽  
Mohamed Souhassou ◽  
Masaki Takata ◽  
Kenichi Kato ◽  
...  
Keyword(s):  
Powder Diffraction ◽  
Dipole Moments ◽  
Membered Ring ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Crystallographic Study ◽  
Synchrotron Powder Diffraction ◽  
Ring Channel ◽  
New Phase

The crystal structure of a new phase consisting of the inclusion of the hyperpolarizable molecule p-N,N-dimethylnitroaniline (dimethyl-para-nitroaniline or dmpNA) in the large-pore zeolite mordenite (MOR) has been determined from high-resolution synchrotron powder diffraction at 300 and 90 K. The unit-cell parameters and space group at 300 K are similar to those of as-synthesized mordenite. The crystallographic study indicates that the MOR straight channels are almost fully loaded with molecules that are disordered over eight symmetry-related sites. As expected, the molecules are located in the large 12-membered ring channel, at the intersection with the secondary eight-membered channel with which they might form hydrogen bonds. The elongation axes (and then the dipole moments) of the molecules are slightly tilted (28.57°) from [001]. The configuration found suggests an interaction of dmpNA with framework O atoms through its methyl groups.

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