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Initial Electron-density Maps (initial + electron-density_map)

Distribution by Scientific Domains

Chemistry	100%

Selected Abstracts

Multivariate phase combination improves automated crystallographic model building

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2010
Pavol Skubák
Density modification is a standard technique in macromolecular crystallography that can significantly improve an initial electron-density map. To obtain optimal results, the initial and density-modified map are combined. Current methods assume that these two maps are independent and propagate the initial map information and its accuracy indirectly through previously determined coefficients. A multivariate equation has been derived that no longer assumes independence between the initial and density-modified map, considers the observed diffraction data directly and refines the errors that can occur in a single-wavelength anomalous diffraction experiment. The equation has been implemented and tested on over 100 real data sets. The results are dramatic: the method provides significantly improved maps over the current state of the art and leads to many more structures being built automatically. [source]

Crystallization and preliminary X-ray analysis of human endonuclease 1 (APE1) in complex with an oligonucleotide containing a 5,6-dihydrouracil (DHU) or an ,-anomeric 2,-deoxyadenosine (,dA) modified base

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2010
Pascal Retailleau
The multifunctional human apurinic/apyrimidinic (AP) endonuclease 1 (APE1) is a key enzyme involved in both the base-excision repair (BER) and nucleotide-incision repair (NIR) pathways. In the NIR pathway, APE1 incises DNA 5, to a number of oxidatively damaged bases. APE1 was crystallized in the presence of a 15-mer DNA containing an oxidatively damaged base in a single central 5,6-dihydrouracil (DHU)·T or ,-anomeric 2,-deoxyadenosine (,dA)·T base pair. Diffraction data sets were collected to 2.2 and 2.7,Å resolution from DNA-DHU,APE1 and DNA-,dA,APE1 crystals, respectively. The crystals were isomorphous and contained one enzyme molecule in the asymmetric unit. Molecular replacement was performed and the initial electron-density maps revealed that in both complexes APE1 had crystallized with a degradation DNA product reduced to a 6-mer, suggesting that NIR and exonuclease reactions occurred prior to crystallization. [source]

Crystallization and preliminary X-ray diffraction analysis of mouse galectin-4 N-terminal carbohydrate recognition domain in complex with lactose

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2008
Veronika Krej, íková
Galectin-4 is thought to play a role in the process of tumour conversion of cells of the alimentary tract and the breast tissue; however, its exact function remains unknown. With the aim of elucidating the structural basis of mouse galectin-4 (mGal-4) binding specificity, we have undertaken X-ray analysis of the N-terminal domain, CRD1, of mGal-4 in complex with lactose (the basic building block of known galectin-4 carbohydrate ligands). Crystals of CRD1 in complex with lactose were obtained using vapour-diffusion techniques. The crystals belong to tetragonal space group P4212 with unit-cell parameters a = 91.1, b = 91.16, c = 57.10,Å and preliminary X-ray diffraction data were collected to 3.2,Å resolution. An optimized crystallization procedure and cryocooling protocol allowed us to extend resolution to 2.1,Å. Structure refinement is currently under way; the initial electron-density maps clearly show non-protein electron density in the vicinity of the carbohydrate binding site, indicating the presence of one lactose molecule. The structure will help to improve understanding of the binding specificity and function of the potential colon cancer marker galectin-4. [source]

Crystallization and preliminary structure analysis of the blue laccase from the ligninolytic fungus Panus tigrinus

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2005
Marta Ferraroni
The blue laccase from the white-rot basidiomycete fungus Panus tigrinus, an enzyme involved in lignin biodegradation, has been crystallized. P. tigrinus laccase crystals grew within one week at 296,K using the sitting-drop vapour-diffusion method in 22%(w/v) PEG 4000, 0.2,M CaCl2, 100,mM Tris,HCl pH 7.5. The crystals belong to the monoclinic space group P21, with unit-cell parameters a = 54.2, b = 111.6, c = 97.1, , = 97.7°, and contain 46% solvent. A complete native data set was collected to 1.4,Å resolution at the copper edge. Molecular replacement using the Coprinus cinereus laccase structure (PDB code 1hfu) as a starting model was performed and initial electron-density maps revealed the presence of a full complement of copper ions. Model refinement is in progress. The P. tigrinus laccase structural model exhibits the highest resolution available to date and will assist in further elucidation of the catalytic mechanism and electron-transfer processes for this class of enzymes. [source]