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Atomic Resolution Data (atomic + resolution_data)
Selected AbstractsApplications of ACORN to data at 1.45 Å resolutionJOURNAL OF SYNCHROTRON RADIATION, Issue 1 2004V. Rajakannan One of the main interests in the molecular biosciences is in understanding structure,function relations and X-ray crystallography plays a major role in this. ACORN can be used as a comprehensive and efficient phasing procedure for the determination of protein structures when atomic resolution data are available. An initial model can automatically be built by ARP/wARP followed by REFMAC for refinement. The , helices and , sheets occurring in many protein structures can be taken as starting fragments for structure solution in ACORN. ACORN, along with ARP/wARP followed by REFMAC, can be an ab initio method for solving protein structure for which data are better than 1.2 Å (atomic resolution). Attempts are here made in extending its applications to real data at 1.45 Å resolution and also to truncated data at 1.6 Å resolution. Two previously known structures, congerin II and alkaline cellulase N257, were resolved using the above approach. Automatic structure solution, phasing and refinement for real data at still lower resolutions for proteins of various complexities are being carried out. Data mining of the secondary structural features using PDB is being carried out for this new approach for `seed-phasing' to ACORN. [source] Atomic resolution studies of carbonic anhydrase IIACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2010Craig A. Behnke Carbonic anhydrase has been well studied structurally and functionally owing to its importance in respiration. A large number of X-ray crystallographic structures of carbonic anhydrase and its inhibitor complexes have been determined, some at atomic resolution. Structure determination of a sulfonamide-containing inhibitor complex has been carried out and the structure was refined at 0.9,Å resolution with anisotropic atomic displacement parameters to an R value of 0.141. The structure is similar to those of other carbonic anhydrase complexes, with the inhibitor providing a fourth nonprotein ligand to the active-site zinc. Comparison of this structure with 13 other atomic resolution (higher than 1.25,Å) isomorphous carbonic anhydrase structures provides a view of the structural similarity and variability in a series of crystal structures. At the center of the protein the structures superpose very well. The metal complexes superpose (with only two exceptions) with standard deviations of 0.01,Å in some zinc,protein and zinc,ligand bond lengths. In contrast, regions of structural variability are found on the protein surface, possibly owing to flexibility and disorder in the individual structures, differences in the chemical and crystalline environments or the different approaches used by different investigators to model weak or complicated electron-density maps. These findings suggest that care must be taken in interpreting structural details on protein surfaces on the basis of individual X-ray structures, even if atomic resolution data are available. [source] High-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D2 -symmetric active siteACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2006Narendra Narayana R67 plasmid-encoded dihydrofolate reductase (R67 DHFR) is an NADPH-dependent homotetrameric enzyme that catalyzes the reduction of dihydrofolate to tetrahydrofolate. The amino-acid sequence and molecular architecture of R67 DHFR and its inhibitory properties toward folate analogues are different from those of chromosomal DHFR. Here, the crystal structure of R67 DHFR refined using 1.1,Å resolution data is presented. Blocked full-matrix least-squares refinement without restraints resulted in a final R factor of 11.4%. The anisotropic atomic displacement parameters analyzed by Rosenfield matrices and translation,libration,screw validation suggested four quasi-rigid domains. A total of ten C,,HO hydrogen bonds were identified between the ,-strands. There is reasonable structural evidence that His62 is not protonated in the tetramer, which is in accord with previous pH-profile studies. The side chain of Gln67 that protrudes into the active site exhibits dual conformation, a feature noticed for the first time owing to the availability of atomic resolution data. The R67 DHFR active site is unique: it has D2 symmetry and is a large active site with a pentagonal network of water molecules and exposure of backbone atoms to solvent; the central pore is favorable for planar ring-stacking interactions. The geometrical shape, overall symmetry, local asymmetry and waters appear to dominate the binding of ligands, catalysis and inhibition. [source] Direct methods and protein crystallography at low resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2000Christopher J. Gilmore The tools of modern direct methods are examined and their limitations for solving protein structures discussed. Direct methods need atomic resolution data (1.1,1.2,Å) for structures of around 1000 atoms if no heavy atom is present. For low-resolution data, alternative approaches are necessary and these include maximum entropy, symbolic addition, Sayre's equation, group scattering factors and electron microscopy. [source] | ||||||||||