Second Crystal Form (second + crystal_form)

Distribution by Scientific Domains

Selected Abstracts

Structure determination of the minimal complex between Tfb5 and Tfb2, two subunits of the yeast transcription/DNA-repair factor TFIIH: a retrospective study

Denis E. Kainov
Tfb5 interacts with the Tfb2 subunit of the general transcription factor TFIIH to ensure efficient nucleotide-excision repair in eukaryotes. The crystal structure of the complex between Tfb5 and the C-terminal region of Tfb2 (Tfb2C) from Saccharomyces cerevisiae has recently been reported. Here, the structure-determination process is described as a case study. Although crystals were obtained readily, it was not possible to determine experimental phases from a first crystal form (Tfb2412,513,Tfb52,72) that diffracted to 2.6,┼ resolution. Shortening of the Tfb2C from its N-terminus was decisive and modified the crystal packing, leading to a second crystal form (Tfb2435,513,Tfb52,72). These crystals diffracted to 1.7,┼ resolution with excellent mosaicity and allowed structure determination by conventional approaches using heavy atoms. The refined structure from the second crystal form was used to solve the structure of the first crystal form by molecular replacement. Comparison of the two structures revealed that the N-terminal region of Tfb2C and (to a lesser extent) the C-terminal region of Tfb5 contributed to the crystal packing. A detailed analysis illustrates how variation in domain boundaries influences crystal packing and quality. [source]

Pseudosymmetry, high copy number and twinning complicate the structure determination of Desulfovibrio desulfuricans (ATCC 29577) flavodoxin

Megan Guelker
The crystal structure of oxidized flavodoxin from Desulfovibrio desulfuricans (ATCC 29577) was determined by molecular replacement in two crystal forms, P3121 and P43, at 2.5 and 2.0,┼ resolution, respectively. Structure determination in space group P3121 was challenging owing to the presence of pseudo-translational symmetry and a high copy number in the asymmetric unit (8). Initial phasing attempts in space group P3121 by molecular replacement using a poor search model (46% identity) and multi-wavelength anomalous dispersion were unsuccessful. It was necessary to solve the structure in a second crystal form, space group P43, which was characterized by almost perfect twinning, in order to obtain a suitable search model for molecular replacement. This search model with complementary approaches to molecular replacement utilizing the pseudo-translational symmetry operators determined by analysis of the native Patterson map facilitated the selection and manual placement of molecules to generate an initial solution in the P3121 crystal form. During the early stages of refinement, application of the appropriate twin law, (,h, ,k, l), was required to converge to reasonable R -factor values despite the fact that in the final analysis the data were untwinned and the twin law could subsequently be removed. The approaches used in structure determination and refinement may be applicable to other crystal structures characterized by these complicating factors. The refined model shows flexibility of the flavin mononucleotide coordinating loops indicated by the isolation of two loop conformations and provides a starting point for the elucidation of the mechanism used for protein-partner recognition. [source]

Molecular complementarity between tetracycline and the GTPase active site of elongation factor Tu

Susan E. Heffron
Two crystal forms of a complex between trypsin-modified elongation factor Tu,MgGDP from Escherichia coli and the antibiotic tetracycline have been solved by X-ray diffraction analysis to resolutions of 2.8 and 2.1,┼, respectively. In the P21 form, cocrystals were grown from a solution mixture of the protein and tetracycline. Six copies of the trypsin-modified EF-Tu,MgGDP,tetracycline complex are arranged as three sets of dimers in the asymmetric unit. In the second crystal form, tetracycline was diffused into P43212 crystals, resulting in a monomeric complex in the asymmetric unit. Atomic coordinates have been refined to crystallographic R factors of 18.0% for the P21 form and 20.0% for the P43212 form. In both complexes, tetracycline makes significant interactions with the GTPase active site of EF-Tu. The phenoldiketone moiety of tetracycline interacts directly with the Mg2+, the ,-şphosphate group of GDP and two amino acids, Thr25 and Asp80, which are conserved in the GX4GKS/T and DX2G sequence motifs found in all GTPases and many ATPases. The molecular complementarity, previously unrecognized between invariant groups present in all GTPase/ATPases and the active moiety of tetracycline, may have wide-ranging implications for all drugs containing the phenoldiketone moiety as well as for the design of new compounds targeted against a broad range of GTPases or ATPases. [source]

Crystallization of the Mycobacterium tuberculosis cell-division protein FtsZ

Adelaine K. W. Leung
Mycobacterium tuberculosis FtsZ (MtbFtsZ), an essential protein in bacterial cell division, has been crystallized in the presence of a new inhibitor of MtbFtsZ polymerization and GTPase activity, ethyl (6-şamino-2,3-dihydro-4-phenyl-1H -pyrido[4,3- b][1,4]diazepin-8-yl)carbamate (SRI-7614). Crystals of the MtbFtsZ,SRI-7614 complex (form I, 30% polyethylene glycol 4000, 0.1,M sodium citrate pH 5.6, 0.2,M NH4OAc, 293,K) belong to space group P61 or P65, with unit-cell parameters a = 88.78, c = 178.02,┼, and diffract to 2.3,┼ resolution. A second crystal form, of the GDP complex, grows in the presence or absence of Mg2+ from PEG 4000 at 277,K or from (NH4)2SO4 at 293,K, respectively (form II, space group P6222 or P6422, with unit-cell parameters a = 135.02, c = 328.97,┼ or a = 129.30, c = 327.97,┼, respectively). Complete data sets to ,7,┼ resolution have been collected from both. Exceptional form II crystals diffract to at least 4.5,┼ resolution. Determination of the MtbFtsZ structure may advance the design of improved inhibitors of FtsZ polymerization. [source]

Production, crystallization and preliminary X-ray diffraction analysis of the allergen Can,f,2 from Canis familiaris

Chaithanya Madhurantakam
The allergen Can f 2 from dog (Canis familiaris) present in saliva, dander and fur is an important cause of allergic sensitization worldwide. Here, the production, isolation, crystallization and preliminary X-ray diffraction analysis of two crystal forms of recombinant Can f 2 are reported. The first crystal form belonged to space group C222, with unit-cell parameters a = 68.7, b = 77.3, c = 65.1,┼, and diffracted to 1.55,┼ resolution, while the second crystal form belonged to space group C2, with unit-cell parameters a = 75.7, b = 48.3, c = 68.7,┼, , = 126.5░, and diffracted to 2.1,┼ resolution. Preliminary data analysis indicated the presence of a single molecule in the asymmetric unit for both crystal forms. [source]

Crystallization and preliminary X-ray diffraction analysis of the Fab fragment of WO2, an antibody specific for the A, peptides associated with Alzheimer's disease

Kwok S. Wun
The murine monoclonal antibody WO2 specifically binds the N-terminal region of the amyloid , peptide (A,) associated with Alzheimer's disease. This region of A, has been shown to be the immunodominant B-cell epitope of the peptide and hence is considered to be a basis for the development of immunotherapeutic strategies against this prevalent cause of dementia. Structural studies have been undertaken in order to characterize the molecular basis for antibody recognition of this important epitope. Here, details of the crystallization and X-ray analysis of the Fab fragment of the unliganded WO2 antibody in two crystal forms and of the complexes that it forms with the truncated A, peptides A,1,16 and A,1,28 are presented. These crystals were all obtained using the hanging-drop vapour-diffusion method at 295,K. Crystals of WO2 Fab were grown in polyethylene glycol solutions containing ZnSO4; they belonged to the orthorhombic space group P212121 and diffracted to 1.6,┼ resolution. The complexes of WO2 Fab with either A,1,16 or A,1,28 were cocrystallized from polyethylene glycol solutions. These two complex crystals grew in the same space group, P212121, and diffracted to 1.6,┼ resolution. A second crystal form of WO2 Fab was grown in the presence of the sparingly soluble A,1,42 in PEG 550 MME. This second form belonged to space group P21 and diffracted to 1.9,┼ resolution. [source]