scholarly journals Preliminary crystallographic analysis of the N-terminal domain of FILIA, a protein essential for embryogenesis

2010 ◽  
Vol 66 (9) ◽  
pp. 1111-1114
Author(s):  
Juke Wang ◽  
Tong-Cun Zhang ◽  
Xinqi Liu
Keyword(s):  
Diffraction Data ◽  
Early Stage ◽  
Crystal Form ◽  
Crystallographic Analysis ◽  
Orthorhombic Crystal ◽  
Crystal Forms ◽  
Terminal Domain ◽  
Peg 4000 ◽  
Tetragonal Crystals ◽  
Crystallization Conditions

FILIA is a component of the subcortical maternal complex that is essential for early stage embryogenesis. Its 6×His-tagged N-terminal domain was expressed inEscherichia coliand purified to homogeneity. Two types of crystals formed under different crystallization conditions during screening. Orthorhombic crystals appeared in a solution containing 1.4 Mammonium sulfate, 0.1 MTris pH 8.2 and 12% glycerol, while tetragonal crystals were obtained using 15% PEG 4000 mixed with 0.1 MHEPES pH 7.5 and 15% 2-propanol. High-quality diffraction data were collected from the two crystal forms to resolutions of 1.8 and 2.2 Å, respectively, using synchrotron radiation. The Matthews coefficients indicated that theP212121andP41212 crystals contained two molecules and one molecule per asymmetric unit, respectively. A selenomethionine-substituted sample failed to crystallize under the native conditions, but another orthorhombic crystal form was obtained under different conditions and anomalous diffraction data were collected.

Structure of a backtracked state reveals conformational changes similar to the state following nucleotide incorporation in human norovirus polymerase

2014 ◽  
Vol 70 (12) ◽  
pp. 3099-3109 ◽  
Author(s):  
Dmitry Zamyatkin ◽  
Chandni Rao ◽  
Elesha Hoffarth ◽  
Gabriela Jurca ◽  
Hayeong Rho ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Covalent Bond ◽  
Crystal Form ◽  
Phosphoryl Group ◽  
Nucleoside Triphosphate ◽  
Orthorhombic Crystal ◽  
Crystal Forms ◽  
Terminal Nucleotide ◽  
Thumb Domain

The RNA-dependent RNA polymerase (RdRP) from norovirus (NV) genogroup II has previously been crystallized as an apoenzyme (APO1) in multiple crystal forms, as well as as a pre-incorporation ternary complex (PRE1) bound to Mn2+, various nucleoside triphosphates and an RNA primer-template duplex in an orthorhombic crystal form. When crystallized under near-identical conditions with a slightly different RNA primer/template duplex, however, the enzyme–RNA complex forms tetragonal crystals (anisotropic data,dmin≃ 1.9 Å) containing a complex with the primer/template bound in a backtracked state (BACK1) similar to a post-incorporation complex (POST1) in a step of the enzymatic cycle immediately following nucleotidyl transfer. The BACK1 conformation shows that the terminal nucleotide of the primer binds in a manner similar to the nucleoside triphosphate seen in the PRE1 complex, even though the terminal two phosphoryl groups in the triphosphate moiety are absent and a covalent bond is present between the α-phosphoryl group of the terminal nucleotide and the 3′-oxygen of the penultimate nucleotide residue. The two manganese ions bound at the active site coordinate to conserved Asp residues and the bridging phosphoryl group of the terminal nucleotide. Surprisingly, the conformation of the thumb domain in BACK1 resembles the open APO1 state more than the closed conformation seen in PRE1. The BACK1 complex thus reveals a hybrid state in which the active site is closed while the thumb domain is open. Comparison of the APO1, PRE1 and BACK1 structures of NV polymerase helps to reveal a more complete and complex pathway of conformational changes within a single RdRP enzyme system. These conformational changes lend insight into the mechanism of RNA translocation following nucleotidyl transfer and suggest novel approaches for the development of antiviral inhibitors.

scholarly journals Structures ofEscherichia colitryptophanase in holo and `semi-holo' forms

2015 ◽  
Vol 71 (3) ◽  
pp. 286-290 ◽  
Author(s):  
Anna Kogan ◽  
Leah Raznov ◽  
Garik Y. Gdalevsky ◽  
Rivka Cohen-Luria ◽  
Orna Almog ◽  
...  
Keyword(s):  
Pyridoxal Phosphate ◽  
Crystal Form ◽  
Asymmetric Unit ◽  
Sulfate Ions ◽  
Crystal Forms ◽  
Cell Parameters ◽  
Open Conformation ◽  
Crystallization Conditions ◽  
Tyrosine Phenol Lyase ◽  
Polypeptide Chains

Two crystal forms ofEscherichia colitryptophanase (tryptophan indole-lyase, Trpase) were obtained under the same crystallization conditions. Both forms belonged to the same space groupP43212 but had slightly different unit-cell parameters. The holo crystal form, with pyridoxal phosphate (PLP) bound to Lys270 of both polypeptide chains in the asymmetric unit, diffracted to 2.9 Å resolution. The second crystal form diffracted to 3.2 Å resolution. Of the two subunits in the asymmetric unit, one was found in the holo form, while the other appeared to be in the apo form in a wide-open conformation with two sulfate ions bound in the vicinity of the active site. The conformation of all holo subunits is the same in both crystal forms. The structures suggest that Trpase is flexible in the apo form. Its conformation partially closes upon binding of PLP. The closed conformation might correspond to the enzyme in its active state with both cofactor and substrate bound in a similar way as in tyrosine phenol-lyase.

Crystallization and preliminary X-ray analysis of the Tet-repressor/operator complex

1998 ◽  
Vol 54 (1) ◽  
pp. 99-100 ◽  
Author(s):  
Peter Orth ◽  
Claudia Alings ◽  
Dirk Schnappinger ◽  
Wolfram Saenger ◽  
Winfried Hinrichs
Keyword(s):  
Molecular Replacement ◽  
Crystal Forms ◽  
X Ray ◽  
Space Groups ◽  
Class D ◽  
Peg 4000 ◽  
Operator Sequence ◽  
Tet Repressor ◽  
Crystallization Conditions ◽  
Repressor Molecule

Three crystal forms of the repressor protein TetR class D in complex with the palindromic 17 bp operator sequence containing T overhangs on both sides were obtained by hanging-drop vapor-diffusion methods using PEG 4000 and PEG monomethylether 5000 as precipitants. Although the crystallization conditions were very similar, up to three different crystal forms were observed in the same drop. The space groups are monoclinic C2, P21 and hexagonal P6122. The asymmetric units of the latter two crystal forms contain one repressor–operator complex. The crystal structures of these forms were solved by molecular replacement using the Tet-repressor molecule of the complex with tetracycline as a search model.

Unravelling the chemical basis of the bathochromic shift in the lobster carapace; new crystal structures of unbound astaxanthin, canthaxanthin and zeaxanthin

2007 ◽  
Vol 63 (2) ◽  
pp. 328-337 ◽  
Author(s):  
Giuditta Bartalucci ◽  
Jennifer Coppin ◽  
Stuart Fisher ◽  
Gillian Hall ◽  
John R. Helliwell ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Crystal Packing ◽  
Bathochromic Shift ◽  
Crystal Form ◽  
Crystal Forms ◽  
Bonding Interaction ◽  
Crystallization Conditions ◽  
Intermolecular Distances

The crystal structures of the unbound carotenoids, synthetic astaxanthin (3S,3′S:3R,3′S:3R,3′R in a 1:2:1 ratio), canthaxanthin and (3R,3′S, meso)-zeaxanthin are compared with each other and the protein bound astaxanthin molecule in the carotenoprotein, β-crustacyanin. Three new crystal forms of astaxanthin have been obtained, using different crystallization conditions, comprising a chloroform solvate, a pyridine solvate and an unsolvated form. In each structure, the astaxanthin molecules, which are similar to one another, are centrosymmetric and adopt the 6-s-cis conformation; the end rings are bent out of the plane of the polyene chain by angles of −42.6 (5), −48.9 (5) and −50.4 (3)°, respectively, and are disordered, showing the presence of both R and S configurations (in a 1:1 ratio). In the crystal packing of the chloroform and pyridine solvates, the astaxanthin molecules show pair-wise end-to-end intermolecular hydrogen bonding of the adjacent 3-hydroxyl and 4-keto oxygens, whereas in the unsolvated crystal form, the hydrogen-bonding interaction is intermolecular. In addition, there are intermolecular C—H hydrogen bonds in all three structures. The canthaxanthin structure, measured at 100 and 293 K, also adopts the 6-s-cis conformation, but with disorder of one end ring only. The rotation of the end rings out of the plane of the polyene chains (ca −50 ° for each structure) is similar to that of astaxanthin. A number of possible C—H hydrogen bonds to the keto O atoms are also observed. (3R,3′S, meso)-zeaxanthin is centrosymmetric with a C5—C6—C7—C8 torsion angle of −74.9 (3)°; the molecules show pair-wise hydrogen bonding between the hydroxyl O atoms. In addition, for all the crystal structures the polyene chains were arranged one above the other, with intermolecular distances of 3.61–3.79 Å, indicating the presence of π-stacking interactions. Overall, these six crystal structures provide an ensemble of experimentally derived results that allow several key parameters, thought to influence colour tuning of the bathochromic shift of astaxanthin in crustacyanin, to be varied. The fact that the colour of each of the six crystals remains red, rather than turning blue, is therefore especially significant.

Polymorphous crystallization and diffraction of threonine deaminase from Escherichia coli

1998 ◽  
Vol 54 (3) ◽  
pp. 467-469 ◽  
Author(s):  
D. Travis Gallagher ◽  
Edward Eisenstein ◽  
Kathryn E. Fisher ◽  
James Zondlo ◽  
Diana Chinchilla ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Diffraction Data ◽  
Crystal Form ◽  
Data Sets ◽  
Threonine Deaminase ◽  
Crystal Forms ◽  
Space Group ◽  
Regulatory Functions

The biosynthetic threonine deaminase from Escherichia coli, an allosteric tetramer with key regulatory functions, has been crystallized in several crystal forms. Two distinct forms, both belonging to either space group P3121 or P3221, with different sized asymmetric units that both contain a tetramer, grow under identical conditions. Diffraction data sets to 2.8 Å resolution (native) and 2.9 Å resolution (isomorphous uranyl derivative) have been collected from a third crystal form in space group I222.

Analysis of multiple crystal forms ofBacillus subtilisBacB suggests a role for a metal ion as a nucleant for crystallization

2010 ◽  
Vol 66 (5) ◽  
pp. 635-639 ◽  
Author(s):  
M. Rajavel ◽  
B. Gopal
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Crystal Packing ◽  
Crystal Form ◽  
Monoclinic Crystal ◽  
Crystal Forms ◽  
Tetragonal Crystal ◽  
Crystallization Conditions ◽  
Surface Metal ◽  
X Ray Absorption

Bacillus subtilisBacB is an oxidase that is involved in the production of the antibiotic bacilysin. This protein contains two double-stranded β-helix (cupin) domains fused in a compact arrangement. BacB crystallizes in three crystal forms under similar crystallization conditions. An interesting observation was that a slight perturbation of the crystallization droplet resulted in the nucleation of a different crystal form. An X-ray absorption scan of BacB suggested the presence of cobalt and iron in the crystal. Here, a comparative analysis of the different crystal forms of BacB is presented in an effort to identify the basis for the different lattices. It is noted that metal ions mediating interactions across the asymmetric unit dominate the different packing arrangements. Furthermore, a normalizedB-factor analysis of all the crystal structures suggests that the solvent-exposed metal ions decrease the flexibility of a loop segment, perhaps influencing the choice of crystal form. The residues coordinating the surface metal ion are similar in the triclinic and monoclinic crystal forms. The coordinating ligands for the corresponding metal ion in the tetragonal crystal form are different, leading to a tighter packing arrangement. Although BacB is a monomer in solution, a dimer of BacB serves as a template on which higher order symmetrical arrangements are formed. The different crystal forms of BacB thus provide experimental evidence for metal-ion-mediated lattice formation and crystal packing.

The structure of dihydrodipicolinate reductase (DapB) fromMycobacterium tuberculosisin three crystal forms

2009 ◽  
Vol 66 (1) ◽  
pp. 61-72 ◽  
Author(s):  
Robert Janowski ◽  
Georgia Kefala ◽  
Manfred S. Weiss
Keyword(s):  
Conformational Change ◽  
Normal Modes ◽  
Low Frequency ◽  
Pyridine Nucleotide ◽  
Crystal Form ◽  
Orthorhombic Crystal ◽  
Monoclinic Crystal ◽  
Crystal Forms ◽  
Comparison Of The Results ◽  
Unstable Product

Dihydrodipicolinate reductase (DHDPR, DapB) is an enzyme that belongs to the L-lysine biosynthetic pathway. DHDPR reduces the α,β-unsaturated cyclic imine 2,3-dihydrodipicolinic acid to yield the compound 2,3,4,5-tetrahydrodipicolinic acid in a pyridine nucleotide-dependent reaction. The substrate of this reaction is the unstable product of the preceding enzyme dihydrodipicolinate synthase (DHDPS, DapA). Here, the structure of apo-DHDPR fromMycobacterium tuberculosisis reported in two orthorhombic crystal forms, as well as the structure of DHDPR fromM. tuberculosisin complex with NADH in a monoclinic crystal form. A comparison of the results with previously solved structures of this enzyme shows that DHDPR undergoes a major conformational change upon binding of its cofactor. This conformational change can be interpreted as one of the low-frequency normal modes of the structure.

scholarly journals Born out of Fire and Ice: Polymorph Studies of the Antiviral Famciclovir

Crystals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 129
Author(s):  
Liana Vella-Zarb ◽  
Ulrich Baisch
Keyword(s):  
Variable Temperature ◽  
Chemical Properties ◽  
Crystal Form ◽  
X Ray Diffraction ◽  
Crystal Forms ◽  
X Ray ◽  
Physical Chemical ◽  
Diffraction Patterns ◽  
Crystalline Forms

There is much interest and focus on solid forms of famciclovir. However, in spite of the abundance of reported differences in oral bioavailability, compressibility, and other physical–chemical properties of the various crystal forms of this drug, very little precise structural analysis is available in the literature to date. The form used in the commercial formulation is the anhydrous form I. Patents and patent applications report three different anhydrous crystalline forms on the basis of unindexed powder diffraction patterns. Single-crystal and variable-temperature X-ray diffraction experiments using the commercially available anhydrous form of famciclovir were carried out and led not only to the crystal structure determination of the anhydrous form I, but also to discovery of a new crystal form of anhydrous famciclovir from powder data.

scholarly journals Tunable Nonlinear Optical Property of MnS Nanoparticles with Different Size and Crystal Form

Nanomaterials ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 34
Author(s):  
Zhihao Zhang ◽  
Pengchao Li ◽  
Yuzong Gu
Keyword(s):  
Optical Property ◽  
Nonlinear Optical ◽  
Nonlinear Optical Property ◽  
Nonlinear Refraction ◽  
Synthesis Method ◽  
Crystal Form ◽  
Optical Nonlinearity ◽  
Photon Absorption ◽  
Third Order ◽  
Crystal Forms

It is significant to study the reason that semiconductor material has adjustable third-order optical nonlinearity through crystal form and dimensions are changed. αMnS nanoparticles with different crystal forms and sizes were successfully prepared by one-step hydrothermal synthesis method and their size-limited third-order nonlinear optical property was tested by Z-scan technique with 30 ps laser pulses at 532 nm wavelength. Nanoparticles of different crystal forms exhibited different NLO (nonlinear optical) responses. γMnS had stronger NLO response than αMnS because of higher fluorescence quantum yield. Two-photon absorption and the nonlinear refraction are enhanced as size of nanoparticlesreduced. The nanoparticles had maximum NLO susceptibility which was 3.09 × 10−12 esu. Susceptibility of αMnS increased about nine times than that of largest nanoparticles. However, it was reduced when size was further decreased. This trend was explained by the effects of light induced dipole moments. And defects in αMnS nanoparticles also had effect on this nonlinear process. MnS nanoparticles had potential application value in optical limiting and optical modulation.

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