‘Crystal lattice engineering,’ an approach to engineer protein crystal contacts by creating intermolecular symmetry: Crystallization and structure determination of a mutant human RNase 1 with a hydrophobic interface of leucines

X-ray irradiation on a protein crystal can cause some subtle structural modification on the protein structure even if the radiation dose is much smaller than a dose used for a common crystal structure determination. In some case such structural modification increases ambiguity of structural inspection, and eventually could be an obstacle on the elucidation of structure basis of protein function. Bovine heart cytochrome c oxidase (CcO) is one of such proteins having some problem caused by the radiation damage. The proton pumping of CcO is coupled with O2 reduction at the O2 reduction site, thus accurate structure determination of bound ligand as well as CcO itself is very important. Whereas accurate structure determination was impeded by the immediate photolysis of the peroxide ligand upon X-ray irradiation even at a cryogenic temperature[1]. We developed a goniometer based data collection system for the femtosecond crystallography at SACLA (SPring-8 Angstrom Compact free-electron LAser). The femtosecond crystallography is expected to have an advantage in high-resolution and radiation damage free structure determination of very large protein by combined usage of large crystal and femtosecond intense X-ray pulse. In this presentation we are going to show the result of the femtosecond crystallography on the crystal of CcO having large unit cell dimensions. The close inspection of the electron density map calculated at 1.9 Å resolution showed the femtosecond crystallography worked fine for the high resolution and radiation damage free crystal structure determination of CcO.

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Crystal structure and conformational analysis of doxorubicin nitrate

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989018002955 ◽

2018 ◽

Vol 74 (3) ◽

pp. 400-405 ◽

Cited By ~ 1

Author(s):

Logesh Mathivathanan ◽

Guang Yang ◽

Fenfei Leng ◽

Raphael G. Raptis

Keyword(s):

Crystal Structure ◽

Conformational Analysis ◽

Crystal Lattice ◽

Structure Determination ◽

Crystal Structure Determination ◽

Asymmetric Unit ◽

Two Component ◽

Hydrogen Bonded

Crystal structure determination of doxorubicin nitrate, (DoxH)NO3, systematic name (7S,9S)-7-{[(2R,4S,5S,6S)-4-azaniumyl-5-hydroxy-6-methyloxan-2-yl]oxy}-6,9,11-trihydroxy-9-(2-hydroxyacetyl)-4-methoxy-8,10-dihydro-7H-tetracen-5,12-dione nitrate, shows two formula units present in the asymmetric unit. In the crystal lattice, hydrogen-bonded pairs of (DoxH+) cations and segregation of the aglycone and sugar moieties are observed. Inspection of molecular overlays reveals that the conformation of (DoxH)NO3resembles that of DNA-intercalated, but not of protein-docked (DoxH)+. The structure was refined as a two-component twin.

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Synthesis, spectroscopic studies and X-ray structure determination of two mononuclear copper complexes derived from the Schiff base ligand N,N-dimethyl-N'-((5-methyl-1H-imidazol-4-yl)methylene)ethane-1,2-diamine

European Journal of Chemistry ◽

10.5155/eurjchem.10.3.201-208.1881 ◽

2019 ◽

Vol 10 (3) ◽

pp. 201-208

Author(s):

Pokpa Haba ◽

Adama Sy ◽

Farba Bouyagui Tamboura ◽

Mamour Sarr ◽

Ibrahima Elhadji Thiam ◽

...

Keyword(s):

Schiff Base ◽

Crystal Lattice ◽

Structure Determination ◽

Unit Cell ◽

Monoclinic Space Group ◽

Unit Cell Parameters ◽

Space Group ◽

X Ray ◽

Cell Parameters

Reactions of the Schiff base N,N-dimethyl-N'-((5-methyl-1H-imidazol-4-yl)methylene) ethane-1,2-diamine (HL), synthesised in situ, with chloride or thiocyanate copper (II) salt; afforded two new mononuclear complexes, [Cu(HL)Cl2]·H2O (1) and [Cu(HL)(SCN)2] (2). These compounds have been studied and characterized by elemental analysis, IR and UV-Vis spectroscopies, electrochemistry, molar conductivity and room temperature magnetic measurements. Single crystal X-ray structure determination of the complexes revealed the presence of neutral moieties in the asymmetric unit. The mononuclear (1) crystallises in the monoclinic space group P21/c with the following unit cell parameters a = 7.4355(3) Å, b = 7.2952(3) Å, c = 26.2729(11) Å, β = 93.461(4)°, V = 1422.52(10) Å3, Z = 4, R1 = 0.033 and wR2 = 0.082 and the mononuclear complex (2) crystallises in the monoclinic space group C2/c with the following unit cell parameters a = 26.2578(7) Å, b = 7.4334(2) Å, c = 16.6237(5) Å, β = 99.089(3)°, V = 3203.95(16) Å3, Z = 8, R1 = 0.037 and wR2 = 0.104. In both complexes the ligand acts in tridentate fashion and the coordination environment of the copper atom can be described as distorted square pyramidal. The crystal lattice of the complex 1 is stabilized by electrostatic forces of attraction and O–H···Cl, C–H···O, N–H···Cl, and C–H···Cl, hydrogen bonding interactions while the crystal lattice of the complex 2 is stabilized by N–H···S and C–H···N.

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Structure Determination of Echovirus 1

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444998002790 ◽

1998 ◽

Vol 54 (6) ◽

pp. 1261-1272 ◽

Cited By ~ 39

Author(s):

D. J. Filman ◽

M. W. Wien ◽

J. A. Cunningham ◽

J. M. Bergelson ◽

J. M. Hogle

Keyword(s):

Crystal Lattice ◽

Diffraction Pattern ◽

Structure Determination ◽

Atomic Structure ◽

Molecular Replacement ◽

Asymmetric Unit ◽

Space Group ◽

Icosahedral Particle ◽

Packing Analysis

The atomic structure of echovirus 1 (a member of the enterovirus genus of the picornavirus family) has been determined using cryo-crystallography and refined to 3.55 Å resolution. Echovirus 1 crystallizes in space group P22121 with a = 352.45, b = 472.15 and c = 483.20 Å. The crystals contain one full virus particle in the asymmetric unit allowing for 60-fold noncrystallographic symmetry averaging. The diffraction pattern shows strong pseudo-B-centering with reflections with h + l = 2n + 1 being systematically weak or absent below about 6 Å resolution. The size of the unit cell and presence of pseudo-B-centering placed strong constraints on the allowed packing of the icosahedral particle in the crystal lattice. These constraints greatly facilitated the determination of the orientation and position of the virus by reducing the dimensionality of the search, but interactions between the crystallographic and noncrystallographic symmetries rendered the choice of space group ambiguous until very late in the structure determination. This structure determination provides a striking example of the power of packing analysis in molecular replacement and illustrates how subtle interactions between crystallographic and noncrystallographic symmetries can be resolved.

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