July 1996 issue
Cover illustration: NMR solution structure of an Antennapedia homeodomain complex with a 14-base pair operator DNA duplex. The dotted surface outlines a hydrated cavity in the protein-DNA interface.
Refinement at very high resolution using data collected at low temperature has enabled visualization of a complete water-protein interface, a detailed description of the water structure around a protein and patterns of water-protein interactions. Patterns of local water structure include three-, four-, five- and six-membered rings of hydrogen-bonded water molecules.
Cryogenic structure analysis has been applied on IPMDH to find out the physical difference of the thermostability of the native and chimeric mutant.
The structure of diferric duck ovotransferrin is compared with those of serum transferrin. Interactions between domains and lobes are discussed.
An extension for the self-validation Hamilton test is proposed and applied to assess significance of crystallographic refinement. The general case of refinements carried out with different numbers and types of non-linear restraints is examined.
Sampling solubility phase diagrams for optimized crystal growth is most efficient in a coordinate system in which the `nucleation zone' is a rectangle. Suitable orthogonal basis vectors represent the fundamantal determinants of nucleation rate and subsequent growth, respectively.
The alternating octameric RNA containing a 3'-deoxy residue forms an infinite stacked column with the O2' hydroxyl groups hydrogen bonded, usually via two water molecules, to the neighbouring bases, 3' phosphates, the 3' hydroxyl groups or directly to the O4' sugar of the residue on the 3' side.
High-resolution X-ray data, to 1.3 Å resolution, have been used to refine the crystal structure of the electron-tranfer protein amicyanin, a type I copper protein. Structural parameters are compared with the previous 2.0 Å structure, and discrete disorder in the protein is described.
Inexpensive but accurate optimizations of virus crystal structures with high degrees of non-crystallographic symmetry have used the Fourier transforms of arbitary map volumes as reference standards for stereochemically restrained atomic model refinement.
The structure of γD has been refined using high-resolution data and the correct sequence. The intermolecular organization in the lattice is different to βD as a result of critical mutations to surface residues.
X-ray diffuse scattering by a lysozyme crystal is interpreted in terms of rigid-body displacements of the proteins. the comparison with the main-chain B-factor fluctuations allows a quantization of the motion.
The crystal structure of porcine pancreatic spasmolytic polypeptide is refined to 1.95 Å resolution.
New crystals of the signal-transducing protein PII have been obtained in the presence of a number of different effector ligands. the molecular replacement solution for the PII/ATP/2-keto-glutarate crystal is reported.
A simple weighting scheme for macromolecular refinement that is robust with respect to an incomplete atomic model is discussed.
A method for improving estimates of phases from MIR data sets that contain highly correlated errors is discussed.
The crystal structures of human wild-type transthyretin complexed with thyroxine and the weak binding inhibitor 3',5'-dinitro-N-acetyl-thyronine reveal different binding modes for ligand and inhibtor.
Structural details of the DNA nonamer with overhanging G base d(GCGAATTCG) are described. The structure shows for the first time the geometry at a duplex-triplex junction.
Impurities in commercial HEWL totalling 1-6%(w/w) were identified and individually quantified. Gram quantities of HEWL were purified to >99.9%(w/w) by cation-exchange chromatography. Use of purified material led to significant improvement in crystal quality.
Chemical and electrophoretic analysis, X-ray topography and growth kinetics results supported by a numerical model indicate that lysozyme crystals contain a core of approximately 40 μm diameter in which precipitant and protein impurity concentrations are enhanced.
A protocol for converting crystals of the low-diffracting form to the high-diffracting form of the EF-Tu.EF-Ts complex by controlled dehydration is described. The changes in crystal packing between the two forms are also presented.
The specific effect of a structurally related contaminant on the morphology of resulting protein crystals is lessened in gelled growth media as compared with standard ungelled growth media. This effect is discussd interms of the observed high contaminant inclusion in the crystals.
Direct methods are used to phase all reflections up to derivative resolution. The technique proves to be competitive with traditional SIR methods.
Two user-friendly computer programs are described for use in macromolecular X-ray crystallography. xdlMAPMAN provides an interface for electron-density map exchange between some of the most commonly used phase refinement, structure refinement and model-building programs. In addition it contains several options to analyse and abstract such maps. xdlDATAMAN provides simiilar functionality for the analysis and manipulation of macromolecular reflection data sets. Both programs have a simple graphical user interface and their source code has been put into the public domain.
The matching of the known polypeptide sequence to the electron density is a critical step in solving protein structures by the crystallographic method. Tools have been developed to help in defining the placement of the sequence, both qualitatively and quantitatively. They have been tested with good results on two proteins whose structures were solved by the MIR method.
The similarity of protein structures related by non-crystallo-graphic symmetry has been assessed by a variety of methods. Implications for protein structure refinement are discussed.
A space-group error and a register error of the title compound have been corrected. Implications for protein structure refinement are discussed.
The successful crystallization and X-ray analysis of a vanadium-dependent haloperoxidase from the brown algae Ascophyllum nodosum is described.
The 8-amino-7-oxopelargonate synthase cloned from Bacillus sphaericus has been crystallized and a complete X-ray data set has been collected at 3 Å resolution.
Human salivary cystatin has been crystallized by a silica-gel-mediated sititing-drop method.
The chemical synthesis and crystallization of two complementary heptaribonucleotides forming a helix with a G.U base pair is reported. The crystals are suitable for X-ray structure analysis.
The light-producing enzyme firefly luciferase crystallizes as tetragonal needles which diffract to 2 Å resolution.
Concanavalin A was co-crystallized in two crystal forms with methyl 3,6-di-O-(α-D-manopyranosyl)-α-D-mannopyranoside, which is primarily responsible for its high affinity binding of N-linked carbohydrates. one crystal form is suitable for a 2.3 Å resolution structure determination.
Two highly homologous thermostable NADP-dependent bacterial alcohol dehydrogenases in apo-and holo-enzyme forms have been crystallized. Self-rotation function analysis shows that both enzymes are tetramers of 22 symmetry.
Crystallization of hydroxynitrile from Sorghum bicolor. Three different crystal forms were obtained.
New crystals of carboxypeptidase G2 are more amenable to structure determination of this zinc-exopeptidase with anticancer applications.