Monoclinic Crystal Form (monoclinic + crystal_form)

Distribution by Scientific Domains


Selected Abstracts


Monoclinic crystal form of Aspergillus niger,-şamylase in complex with maltose at 1.8,┼ resolution

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2006
A. Vuji
Aspergillus niger,-amylase catalyses the hydrolysis of ,-1,4-glucosidic bonds in starch. It shows 100% sequence identity to the A. oryzae homologue (also called TAKA-amylase), three crystal structures of which have been published to date. Two of them belong to the orthorhombic space group P212121 with one molecule per asymmetric unit and one belongs to the monoclinic space group P21 with three molecules per asymmetric unit. Here, the purification, crystallization and structure determination of A. niger,-amylase crystallized in the monoclinic space group P21 with two molecules per asymmetric unit in complex with maltose at 1.8,┼ resolution is reported. Furthermore, a novel 1.6,┼ resolution orthorhombic crystal form (space group P21212) of the native enzyme is presented. Four maltose molecules are observed in the maltose,,-amylase complex. Three of these occupy active-site subsites ,2 and ,1, +1 and +2 and the hitherto unobserved subsites +4 (Asp233, Gly234) and +5 (Asp235). The fourth maltose molecule binds at the distant binding sites d1 (Tyr382) and d2 (Trp385), also previously unobserved. Furthermore, it is shown that the active-site groove permits different binding modes of sugar units at subsites +1 and +2. This flexibility of the active-site cleft close to the catalytic centre might be needed for a productive binding of substrate chains and/or release of products. [source]


The structure of dihydrodipicolinate reductase (DapB) from Mycobacterium tuberculosis in three crystal forms

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2010
Robert Janowski
Dihydrodipicolinate reductase (DHDPR, DapB) is an enzyme that belongs to the l -lysine biosynthetic pathway. DHDPR reduces the ,,,-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 from Mycobacterium tuberculosis is reported in two orthorhombic crystal forms, as well as the structure of DHDPR from M. tuberculosis in 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. [source]


Structure of a pseudomerohedrally twinned monoclinic crystal form of a pyridoxal phosphate-dependent catalytic antibody

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2005
BÚatrice Golinelli-Pimpaneau
The purification, crystallization and structure determination at 2.3,┼ resolution of the complex of the pyridoxal-5,-phosphate (PLP) dependent catalytic antibody 15A9 with a phosphopyridoxyl- l -alanine (PPL- l -alanine) substrate analogue are described. The crystal belongs to space group P21, with two molecules in the asymmetric unit related by non-crystallographic symmetry. The unit-cell parameters are a = 63.5, b = 81.7, c = 79.3,┼ and , is fortuitously 90░. Refinement of the structure converged at unacceptably high R factors. Although the traditional analysis of intensity distribution did not indicate twinning, pseudomerohedral twinning was revealed by a newer test based on local intensity differences [Padilla & Yeates (2003), Acta Cryst. D59, 1124,1130]. When the potential twinning operator was included in SHELX, the structure could be satisfactorily refined with a twinning fraction of 0.46, indicating a nearly perfect hemihedrally twinned crystal. One of the active sites is occupied by the phosphopyridoxyl- l -alanine ligand, while one iodide ion mimics the cofactor phosphate group in the other. Four other iodide ions are present in the structure: two are involved in specific intermolecular contacts and two dictate the conformation of the CDRH3 loop in each molecule. [source]


Near-atomic resolution analysis of BipD, a component of the type III secretion system of Burkholderia pseudomallei

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2010
M. Pal
Burkholderia pseudomallei, the causative agent of melioidosis, possesses a type III protein secretion apparatus that is similar to those found in Salmonella and Shigella. A major function of these secretion systems is to inject virulence-associated proteins into target cells of the host organism. The bipD gene of B. pseudomallei encodes a secreted virulence factor that is similar in sequence and is most likely to be functionally analogous to IpaD from Shigella and SipD from Salmonella. Proteins in this family are thought to act as extracellular chaperones at the tip of the secretion needle to help the hydrophobic translocator proteins enter the target cell membrane, where they form a pore and may also link the translocon pore with the secretion needle. BipD has been crystallized in a monoclinic crystal form that diffracted X-rays to 1.5,┼ resolution and the structure was refined to an R factor of 16.1% and an Rfree of 19.8% at this resolution. The putative dimer interface that was observed in previous crystal structures was retained and a larger surface area was buried in the new crystal form. [source]


A triclinic crystal form of Escherichia coli 4-diphosphocytidyl-2C -methyl- d -erythritol kinase and reassessment of the quaternary structure

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2010
Justyna Kalinowska-T
4-Diphosphocytidyl-2C -methyl- d -erythritol kinase (IspE; EC 2.7.1.148) contributes to the 1-deoxy- d -xylulose 5-phosphate or mevalonate-independent biosynthetic pathway that produces the isomers isopentenyl diphosphate and dimethylallyl diphosphate. These five-carbon compounds are the fundamental building blocks for the biosynthesis of isoprenoids. The mevalonate-independent pathway does not occur in humans, but is present and has been shown to be essential in many dangerous pathogens, i.e. Plasmodium species, which cause malaria, and Gram-negative bacteria. Thus, the enzymes involved in this pathway have attracted attention as potential drug targets. IspE produces 4-diphosphosphocytidyl-2C -methyl- d -erythritol 2-phosphate by ATP-dependent phosphorylation of 4-diphosphocytidyl-2C -methyl- d -erythritol. A triclinic crystal structure of the Escherichia coli IspE,ADP complex with two molecules in the asymmetric unit was determined at 2,┼ resolution and compared with a monoclinic crystal form of a ternary complex of E. coli IspE also with two molecules in the asymmetric unit. The molecular packing is different in the two forms. In the asymmetric unit of the triclinic crystal form the substrate-binding sites of IspE are occluded by structural elements of the partner, suggesting that the `triclinic dimer' is an artefact of the crystal lattice. The surface area of interaction in the triclinic form is almost double that observed in the monoclinic form, implying that the dimeric assembly in the monoclinic form may also be an artifact of crystallization. [source]


Purification, crystallization and preliminary X-ray analysis of Enterococcus casseliflavus aminoglycoside-2,,-phosphotransferase-IVa

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2010
Marta Toth
The deactivation of aminoglycoside antibiotics by chemical modification is one of the major sources of bacterial resistance to this family of therapeutic compounds, which includes the clinically relevant drugs streptomycin, kanamycin and gentamicin. The aminoglycoside phosphotransferases (APHs) form one such family of enzymes responsible for this resistance. The gene encoding one of these enzymes, aminoglycoside-2,,-phosphotransferase-IVa [APH(2,,)-IVa] from Enterococcus casseliflavus, has been cloned and the protein (comprising 306 amino-acid residues) has been expressed in Escherichia coli and purified. The enzyme was crystallized in three substrate-free forms. Two of the crystal forms belonged to the orthorhombic space group P212121 with similar unit-cell parameters, although one of the crystal forms had a unit-cell volume that was approximately 13% smaller than the other and a very low solvent content of around 38%. The third crystal form belonged to the monoclinic space group P21 and preliminary X-ray diffraction analysis was consistent with the presence of two molecules in the asymmetric unit. The orthorhombic crystal forms of apo APH(2,,)-IVa both diffracted to 2.2,┼ resolution and the monoclinic crystal form diffracted to 2.4,┼ resolution; synchrotron diffraction data were collected from these crystals at SSRL (Stanford, California, USA). Structure determination by molecular replacement using the structure of the related enzyme APH(2,,)-IIa is proceeding. [source]


Crystallization and preliminary crystallographic analysis of cgHle, a homoserine acetyltransferase homologue, from Corynebacterium glutamicum

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2009
Christine T÷lzer
CgHle is an enzyme that is encoded by gene cg0961 from Corynebacterium glutamicum. The physiological function of cgHle is so far unclear. Bioinformatic annotations based on sequence homology indicated that cgHle may be an acetyl-CoA:homoserine acetyl transferase and as such may be involved in methionine biosynthesis, but recent evidence has shown that it is an esterase that catalyzes the hydrolysis of acetyl esters. Here, the crystallization of cgHle in two orthorhombic crystal forms, a trigonal crystal form and a monoclinic crystal form is described. The trigonal crystals have a solvent content of 83.7%, which is one of the highest solvent contents ever found for protein crystals. One of the orthorhombic crystals diffracted X-rays to at least 1.2,┼ resolution. [source]


Crystallization and preliminary X-ray diffraction analysis of BipD, a virulence factor from Burkholderia pseudomallei

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2006
M. J. Knight
Burkholderia pseudomallei, the causative agent of melioidosis, possesses a protein-secretion apparatus that is similar to those found in Salmonella and Shigella. A major function of these secretion systems is to secrete virulence-associated proteins into target cells of the host organism. The BipD gene of B. pseudomallei encodes a secreted virulence factor that is similar in sequence and most likely functionally analogous to IpaD from Shigella and SipD from Salmonella. Thus, the BipD protein is likely to be a component of a type III protein-secretion system (TTSS) in B. pseudomallei. Proteins in the same class as BipD, such as IpaD and SipD, are thought to act as extracellular chaperones to help the hydrophobic translocator proteins enter the target cell membrane, where they form a pore and might even link the translocon pore with the secretion needle. There is evidence that the translocator proteins also bind an integrin which stimulates actin-mediated insertion of the bacterium into the host-cell membrane. Native BipD has been crystallized in a monoclinic crystal form that diffracts X-rays to 2.5,┼ resolution. BipD protein which incorporates selenomethionine (SeMet-BipD) has also been expressed and forms crystals which diffract to a higher resolution of 2.1,┼. [source]


Preliminary characterization of two different crystal forms of acylphosphatase from the hyperthermophile archaeon Sulfolobus solfataricus

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2005
Simone Zuccotti
Acylphosphatase is a ubiquitous small enzyme that was first characterized in mammals. It is involved in the hydrolysis of carboxyl-phosphate bonds in several acylphosphate substrates, such as carbamoylphosphate and 1,3-biphosphoglycerate; however, a consensus on acylphosphatase action in vivo has not yet been reached. Recent investigations have focused on acylphosphatases from lower phyla, such as Drosophila melanogaster and Escherichia coli, in view of the application of these small proteins as models in the study of folding, misfolding and aggregation processes. An acylphosphatase from the hyperthermophilic archaeon Sulfolobus solfataricus has been cloned, expressed and purified. Here, the growth and characterization of a triclinic and a monoclinic crystal form of the hyperthermophilic enzyme are reported; X-ray diffraction data have been collected to 1.27 and 1.90,┼ resolution, respectively. [source]


Analysis of multiple crystal forms of Bacillus subtilis BacB suggests a role for a metal ion as a nucleant for crystallization

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2010
M. Rajavel
Bacillus subtilis BacB is an oxidase that is involved in the production of the antibiotic bacilysin. This protein contains two double-stranded ,-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 normalized B -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. [source]