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.

scholarly journals Expression, purification and crystallization of the phosphate-binding PstS protein fromPseudomonas aeruginosa

2014 ◽  
Vol 70 (7) ◽  
pp. 906-910 ◽  
Author(s):  
Avi Neznansky ◽  
Yarden Opatowsky
Keyword(s):  
Crystal Form ◽  
Phosphate Transport ◽  
Unit Cell ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
Solvent Content ◽  
Space Group ◽  
Cell Parameters ◽  
Crystal Volume

Pseudomonas aeruginosa(PA) infections pose a serious threat to human health. PA is a leading cause of fatal lung infections in cystic fibrosis and immune-suppressed patients, of sepsis in burn victims and of nosocomial infections. An important element in PA virulence is its ability to establish biofilms that evade suppression by the host's immune system and antibiotics. PstS, a periplasmic subunit of the Pst phosphate-transport system of PA, plays a critical role in the establishment of biofilms. In some drug-resistant PA strains, PstS is secreted in large quantities from the bacteria, where it participates in the assembly of adhesion fibres that enhance bacterial virulence. In order to understand the dual function of PstS in biofilm formation and phosphate transport, the crystal structure of PA PstS was determined. Here, the overexpression inEscherichia coliand purification of PA PstS in the presence of phosphate are described. Two crystal forms were obtained using the vapour-diffusion method at 20°C and X-ray diffraction data were collected. The first crystal form belonged to the centred orthorhombic space groupC2221, with unit-cell parametersa= 67.5,b= 151.3,c= 108.9 Å. Assuming the presence of a dimer in the asymmetric unit gives a crystal volume per protein weight (VM) of 2.09 Å3 Da−1and a solvent content of 41%. The second crystal form belonged to the primitive orthorhombic space groupP212121, with unit-cell parametersa= 35.4,b= 148.3,c= 216.7 Å. Assuming the presence of a tetramer in the asymmetric unit gives a crystal volume per protein weight (VM) of 2.14 Å3 Da−1and a solvent content of 42.65%. A pseudo-translational symmetry is present in theP212121crystal form which is consistent with a filamentous arrangement of PstS in the crystal lattice.

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 data collection of the N-terminal domain of the 26S proteasome regulatory subunit p27 and its complex with the ATPase domain of Rpt5 fromMus musculus

2014 ◽  
Vol 70 (5) ◽  
pp. 611-615
Author(s):  
Wentao Diao ◽  
Xue Yang ◽  
Hao Zhou
Keyword(s):  
Unit Cell ◽  
26S Proteasome ◽  
Regulatory Subunit ◽  
Atpase Domain ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

The protein 26S proteasome regulatory subunit p27 is one of the four chaperones that help in the assembly of the 19S regulatory particle (RP) of the 26S proteasome. In the present work, the N-terminus of p27 (residues 1–128) fromMus musculuswas cloned, expressed, purified and crystallized alone and in complex with the C-terminal ATPase domain of Rpt5 (residues 173–442). The crystals of p27(1–128)diffracted to 1.7 Å resolution and belonged to space groupP212121, with unit-cell parametersa= 26.79,b= 30.39,c= 145.06 Å. Resolution-dependent Matthews coefficient probability analysis suggested the presence of only one molecule per asymmetric unit, with 40.5% solvent content and aVMvalue of 2.02 Å3 Da−1. The crystal of the p27(1–128)–Rpt5(173–442)complex diffracted to 4 Å resolution and belonged to space groupP222, with unit-cell parametersa= 75.93,b= 76.08,c= 336.85 Å. The presence of four heterodimers in the asymmetric unit with 53.2% solvent content and aVMvalue of 2.63 Å3 Da−1or five heterodimers in the asymmetric unit with 41.5% solvent content and aVMvalue of 2.10 Å3 Da−1is assumed.

Crystallization and preliminary X-ray analysis of a complex between the Bowman–Birk trypsin inhibitor from barley and porcine pancreatic trypsin

1999 ◽  
Vol 55 (6) ◽  
pp. 1244-1246 ◽  
Author(s):  
Young Sil Kim ◽  
Hyun Kyu Song ◽  
Se Won Suh
Keyword(s):  
Polyethylene Glycol ◽  
Trypsin Inhibitor ◽  
Unit Cell ◽  
X Rays ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
Solvent Content ◽  
X Ray ◽  
Cell Parameters

A 1:2 complex between the Bowman–Birk trypsin inhibitor from barley seeds and porcine pancreatic trypsin has been crystallized at 291 K using polyethylene glycol as precipitant. The crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 67.10, b = 88.38 and c = 203.65 Å. The asymmetric unit contains two monomers of the complex, with a corresponding Vm of 2.41 Å3 Da−1 and a solvent content of 49%. Native data to 2.2 Å resolution have been collected at 100 K using synchrotron X-rays.

scholarly journals Crystallization and X-ray diffraction analysis of anL-arabinonate dehydratase fromRhizobium leguminosarumbv.trifoliiand aD-xylonate dehydratase fromCaulobacter crescentus

2016 ◽  
Vol 72 (8) ◽  
pp. 604-608 ◽  
Author(s):  
Mohammad Mubinur Rahman ◽  
Martina Andberg ◽  
Anu Koivula ◽  
Juha Rouvinen ◽  
Nina Hakulinen
Keyword(s):  
Rhizobium Leguminosarum ◽  
Caulobacter Crescentus ◽  
Sodium Formate ◽  
Unit Cell ◽  
Diffusion Method ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
Space Group ◽  
Cell Parameters

L-Arabinonate dehydratase (EC 4.2.1.25) and D-xylonate dehydratase (EC 4.2.1.82) are two enzymes that are involved in a nonphosphorylative oxidation pathway of pentose sugars. L-Arabinonate dehydratase converts L-arabinonate into 2-dehydro-3-deoxy-L-arabinonate, and D-xylonate dehydratase catalyzes the dehydration of D-xylonate to 2-dehydro-3-deoxy-D-xylonate. L-Arabinonate and D-xylonate dehydratases belong to the IlvD/EDD family, together with 6-phosphogluconate dehydratases and dihydroxyacid dehydratases. No crystal structure of any L-arabinonate or D-xylonate dehydratase is available in the PDB. In this study, recombinant L-arabinonate dehydratase fromRhizobium leguminosarumbv.trifolii(RlArDHT) and D-xylonate dehydratase fromCaulobacter crescentus(CcXyDHT) were heterologously expressed inEscherichia coliand purified by the use of affinity chromatography followed by gel-filtration chromatography. The purified proteins were crystallized using the hanging-drop vapour-diffusion method at 293 K. Crystals ofRlArDHT that diffracted to 2.40 Å resolution were obtained using sodium formate as a precipitating agent. They belonged to space groupP21, with unit-cell parametersa = 106.07,b= 208.61,c= 147.09 Å, β = 90.43°. EightRlArDHT molecules (two tetramers) in the asymmetric unit give aVMvalue of 3.2 Å3 Da−1and a solvent content of 62%. Crystals ofCcXyDHT that diffracted to 2.66 Å resolution were obtained using sodium formate and polyethylene glycol 3350. They belonged to space groupC2, with unit-cell parametersa= 270.42,b= 236.13,c = 65.17 Å, β = 97.38°. FourCcXyDHT molecules (a tetramer) in the asymmetric unit give aVMvalue of 4.0 Å3 Da−1and a solvent content of 69%.

Crystallization and preliminary X-ray studies of metallothionein II from rabbit liver

1999 ◽  
Vol 55 (6) ◽  
pp. 1242-1243 ◽  
Author(s):  
Yu An ◽  
Genpei Li ◽  
Binggen Ru
Keyword(s):  
Sodium Citrate ◽  
Unit Cell ◽  
Rabbit Liver ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Citrate Buffer ◽  
Solvent Content ◽  
X Ray ◽  
Cell Parameters ◽  
Sodium Citrate Buffer

Metallothionein II (Mw = 6.8 kDa), induced by cadmium and purified from rabbit liver, has been crystallized in space group P6222 or P6422. The unit-cell parameters were a = b = 113.4, c = 219.1 Å, α = β = 90.0, γ = 120.0° when crystallized from sodium citrate buffer and a = b = 113.4, c = 219.6 Å, α = β = 90.0, γ = 120.0° when crystallized from Tris–HCl buffer. There are 12 molecules per asymmetric unit and the solvent content is about 57%.

scholarly journals Expression, crystallization and preliminary crystallographic data analysis of PigI, a putativeL-prolyl-AMP ligase from the prodigiosin synthetic pathway inSerratia

2014 ◽  
Vol 70 (5) ◽  
pp. 624-627 ◽  
Author(s):  
Ning Han ◽  
Tingting Ran ◽  
Xiangdi Lou ◽  
Yanyan Gao ◽  
Jianhua He ◽  
...  
Keyword(s):  
Data Analysis ◽  
Catalytic Mechanism ◽  
Unit Cell ◽  
Crystallographic Data ◽  
Biosynthesis Pathway ◽  
Red Pigment ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
Cell Parameters

Prodigiosin, a member of the prodiginines, is a tripyrrole red pigment synthesized bySerratiaand some other microbes. A bifurcated biosynthesis pathway of prodigiosin has been proposed inSerratiain which MBC (4-methoxy-2,2′-bipyrrole-5-carbaldehyde) and MAP (2-methyl-3-N-amyl-pyrrole) are synthesized separately and then condensed by PigC to form prodigiosin. The first step for the synthesis of MBC is the activation of L-proline by PigI, but its catalytic mechanism has remained elusive. To elucidate its mechanism, recombinant PigI was purified and crystallized. Crystals obtained by the sitting-drop method belonged to space groupP1 and diffracted to 2.0 Å resolution, with unit-cell parametersa= 51.2,b= 62.8,c= 91.3 Å, α = 105.1, β = 90.1, γ = 92.2°. Matthews coefficient analysis suggested two molecules in the asymmetric unit, with aVMof 2.6 Å3 Da−1and a solvent content of 52.69%.

Crystallization and preliminary X-ray studies of sialidase L from the leech Macrobdella decora

1998 ◽  
Vol 54 (1) ◽  
pp. 111-113 ◽  
Author(s):  
Yu Luo ◽  
Min-yuan Chou ◽  
Su-chen Li ◽  
Yu-teh Li ◽  
Ming Luo
Keyword(s):  
Escherichia Coli ◽  
Unit Cell ◽  
Data Sets ◽  
Molecular Replacement ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
X Ray ◽  
Cell Parameters ◽  
Mercury Derivative ◽  
Macrobdella Decora

Functional monomeric 83 kDa sialidase L, a NeuAcα2→3Gal-specific sialidase from Macrobdella leech, was expressed in Escherichia coli and readily crystallized by a macroseeding technique. The crystal belongs to space group P1 with unit-cell parameters a = 46.4, b = 69.3, c = 72.5 Å, α = 113.5, β = 95.4 and γ = 107.3°. There is one molecule per unit cell, giving a Vm = 2.4 Å3 Da−1 and a solvent content of 40%. Native and mercury-derivative data sets were collected to 2.0 Å resolution. Threading and molecular-replacement calculations confirmed the existence of a bacterial sialidase-like domain.

Crystallization and preliminary X-ray study of two crystal forms of Klebsiella oxytoca diol dehydratase–cyanocobalamin complex

1999 ◽  
Vol 55 (4) ◽  
pp. 907-909 ◽  
Author(s):  
Jun Masuda ◽  
Tetsuya Yamaguchi ◽  
Takamasa Tobimatsu ◽  
Tetsuo Toraya ◽  
Kyoko Suto ◽  
...  
Keyword(s):  
Klebsiella Oxytoca ◽  
Crystal Form ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Crystal Forms ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Diol Dehydratase ◽  
Replacement Method

Two crystal forms of Klebsiella oxytoca diol dehydratase complexed with cyanocobalamin have been obtained and preliminary crystallographic experiments have been performed. The crystals belong to two different space groups, depending on the crystallization conditions. One crystal (form I) belongs to space group P212121 with unit-cell parameters a = 76.2, b = 122.3, c = 209.6 Å, and diffracts to 2.2 Å resolution using an X-ray beam from a synchrotron radiation source. The other crystal (form II) belongs to space group P21 with unit-cell parameters a = 75.4, b = 132.7, c = 298.8 Å, β = 91.9°, and diffracts to 3.0 Å resolution. For the purpose of structure determination, a heavy-atom derivative search was carried out and some mercuric derivatives were found to be promising. Structure analysis by the multiple isomorphous replacement method is now under way.

scholarly journals Crystallization and preliminary X-ray analysis of human rhinovirus serotype 2 (HRV2)

1999 ◽  
Vol 55 (8) ◽  
pp. 1459-1461 ◽  
Author(s):  
Núria Verdaguer ◽  
Thomas C. Marlovits ◽  
Jerónimo Bravo ◽  
David I. Stuart ◽  
Dieter Blaas ◽  
...  
Keyword(s):  
Potassium Phosphate ◽  
Attachment Site ◽  
Unit Cell ◽  
Human Rhinovirus ◽  
Intercellular Adhesion Molecule ◽  
Upper Respiratory Tract ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Cell Parameters

Human rhinoviruses, the major cause of mild recurrent infections of the upper respiratory tract, are small icosahedral particles. Over 100 different serotypes have been identified. The majority (91 serotypes) use intercellular adhesion molecule 1 as the cell-attachment site; ten serotypes (the minor group) bind to members of the low-density lipoprotein receptor. Three different crystal forms of the minor-group human rhinovirus serotype 2 (HRV2) were obtained by the hanging-drop vapour-diffusion technique using ammonium sulfate and sodium/potassium phosphate as precipitants. Monoclinic crystals, space group P21, diffracted at least to 2.8 Å resolution, and two complete virus particles were located in the crystal asymmetric unit. A second type of crystals had a compact cubic like morphology and diffracted beyond 2.5 Å resolution. These crystals belong to a primitive orthorhombic space group, with unit-cell parameters a = 309.3, b = 353.5, c = 759.6 Å, and contain one virus particle in the asymmetric unit. A third type of crystals, with a prismatic shape and belonging to space group I222, was also obtained under similar crystallization conditions. These latter crystals, with unit-cell parameters a = 308.7, b = 352.2, c = 380.5 Å, diffracted to high resolution (beyond 1.8 Å) and contained 15 protomers per asymmetric unit; this requires that three perpendicular crystal twofold axes coincide with three of the viral particle's dyad axes.

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