Cubic Crystal Form (cubic + crystal_form)

Distribution by Scientific Domains


Selected Abstracts


Crystal packing of a bacteriophage MS2 coat protein mutant corresponds to octahedral particles

PROTEIN SCIENCE, Issue 10 2008
Pavel Plevka
Abstract A covalent dimer of the bacteriophage MS2 coat protein was created by performing genetic fusion of two copies of the gene while removing the stop codon of the first gene. The dimer was crystallized in the cubic F432 space group. The organization of the asymmetric unit together with the F432 symmetry results in an arrangement of subunits that corresponds to T = 3 octahedral particles. The octahedral particles are probably artifacts created by the particular crystal packing. When it is not crystallized in the F cubic crystal form, the coat protein dimer appears to assemble into T = 3 icosahedral particles indistinguishable from the wild-type particles. To form an octahedral particle with closed surface, the dimer subunits interact at sharper angles than in the icosahedral arrangement. The fold of the covalent dimer is almost identical to the wild-type dimer with differences located in loops and in the covalent linker region. The main differences in the subunit packing between the octahedral and icosahedral arrangements are located close to the fourfold and fivefold symmetry axes where different sets of loops mediate the contacts. The volume of the wild-type virions is 7 times bigger than that of the octahedral particles. [source]


Structure of the X (ADRP) domain of nsp3 from feline coronavirus

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2009
Justyna A. Wojdyla
The structure of the X (or ADRP) domain of a pathogenic variant of feline coronavirus (FCoV) has been determined in tetragonal and cubic crystal forms to 3.1 and 2.2, resolution, respectively. In the tetragonal crystal form, glycerol-3-phosphate was observed in the ADP-ribose-binding site. Both crystal forms contained large solvent channels and had a solvent content of higher than 70%. Only very weak binding of this domain to ADP-ribose was detected in vitro. However, the structure with ADP-ribose bound was determined in the cubic crystal form at 3.9, resolution. The structure of the FCoV X domain had the expected macro-domain fold and is the first structure of this domain from a coronavirus belonging to subgroup 1a. [source]


Structures of feline immunodeficiency virus dUTP pyrophosphatase and its nucleotide complexes in three crystal forms

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2000
G. Sridhar Prasad
dUTP pyrophosphatase (dUTPase) cleaves the ,-, phosphodiester of dUTP to form pyrophosphate and dUMP, preventing incorporation of uracil into DNA and providing the substrate for thymine synthesis. Seven crystal structures of feline immunodeficiency virus (FIV) dUTPase in three crystal forms have been determined, including complexes with substrate (dUTP), product (dUMP) or inhibitor (dUDP) bound. The native enzyme has been refined at 1.40, resolution in a hexagonal crystal form and at 2.3, resolution in an orthorhombic crystal form. In the dUDP complex in a cubic crystal form refined at 2.5, resolution, the C-terminal conserved P-loop motif is fully ordered. The analysis defines the roles of five sequence motifs in interaction with uracil, deoxyribose and the ,-, ,- and ,-phosphates. The enzyme utilizes adaptive recognition to bind the ,- and ,-phosphates. In particular, the ,-, phosphodiester adopts an unfavorable eclipsed conformation in the presence of the P-loop. This conformation may be relevant to the mechanism of ,-, phosphodiester bond cleavage. [source]


Structure of N -acetylglucosamine-1-phosphate uridyltransferase (GlmU) from Mycobacterium tuberculosis in a cubic space group

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2009
Sunil Kumar Verma
GlmU is a bifunctional enzyme that catalyzes the final two steps in the biosynthesis of UDP-GlcNAc. Crystals of GlmU from Mycobacterium tuberculosis obtained using ammonium sulfate as a precipitant diffracted poorly (to 3.4, resolution) and displayed an unusually high solvent content (>80%) with sparse crystal packing that resulted in large solvent channels. With one molecule per asymmetric unit, the monomers from three neighbouring asymmetric units related by the crystal threefold formed a biological trimer. Although this is the first report of the structure of GlmU determined in a cubic crystal form, the trimeric arrangement here is similar to that observed for other GlmU structures determined in hexagonal (H3, H32, P6322) space groups. [source]


Structure of the X (ADRP) domain of nsp3 from feline coronavirus

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2009
Justyna A. Wojdyla
The structure of the X (or ADRP) domain of a pathogenic variant of feline coronavirus (FCoV) has been determined in tetragonal and cubic crystal forms to 3.1 and 2.2, resolution, respectively. In the tetragonal crystal form, glycerol-3-phosphate was observed in the ADP-ribose-binding site. Both crystal forms contained large solvent channels and had a solvent content of higher than 70%. Only very weak binding of this domain to ADP-ribose was detected in vitro. However, the structure with ADP-ribose bound was determined in the cubic crystal form at 3.9, resolution. The structure of the FCoV X domain had the expected macro-domain fold and is the first structure of this domain from a coronavirus belonging to subgroup 1a. [source]


Type II dehydroquinase: molecular replacement with many copies

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2008
Kirsty Anne Stewart
Type II dehydroquinase is a small (150-amino-acid) protein which in solution packs together to form a dodecamer with 23 cubic symmetry. In crystals of this protein the symmetry of the biological unit can be coincident with the crystallographic symmetry, giving rise to cubic crystal forms with a single monomer in the asymmetric unit. In crystals where this is not the case, multiple copies of the monomer are present, giving rise to significant and often confusing noncrystallographic symmetry in low-symmetry crystal systems. These different crystal forms pose a variety of challenges for solution by molecular replacement. Three examples of structure solutions, including a highly unusual triclinic crystal form with 16 dodecamers (192 monomers) in the unit cell, are described. Four commonly used molecular-replacement packages are assessed against two of these examples, one of high symmetry and the other of low symmetry; this study highlights how program performance can vary significantly depending on the given problem. In addition, the final refined structure of the 16-dodecamer triclinic crystal form is analysed and shown not to be a superlattice structure, but rather an F -centred cubic crystal with frustrated crystallographic symmetry. [source]