Structure of apo duck ovotransferrin: the structures of the N and C lobes are in the open form

The structure of apo duck ovotransferrin (APODOT) has been determined at a resolution of 4.0 A by the molecular replacement method using the structure of duck ovotransferrin (DOT) as the search model. The DOT structure contains two iron binding sites; one in the N-terminal lobe lying between domains N1 and N2 and one in the C-terminal lobe between domains C1 and C2. Both lobes have a closed structure. Models of various forms of both the N and C lobes were used in the search. The final model was refined to give an R factor of 0.22. The comparison of the structure of APODOT with that of DOT shows that both the N and the C lobes are in an open form, where the N2 and C2 domains undergo large rigid-body rotations of 51.6 and 49.9 degrees relative to the N1 and C1 domains, respectively. The interface between the N and C lobes, which is formed by the N1-C1 contact in the core of the molecule does not change significantly. The DOT molecule may be described in terms of three rigid bodies; the N1 and C1 domains as one rigid body forming the static core of the molecule and the N2 and C2 domains as two other rigid bodies which, on the release of iron, move away from the static core of the molecule to form the open structure of APODOT.

Crystallization and preliminary X-ray studies on Candida cylindracea lipase

As part of the programme to understand the mechanism and specificity of lipase enzymes used in biotransformation reactions, the lipase from Candida cylindracea has been purified and crystallized. This lipase has been widely used by organic chemists for hydrolysis and esterification reactions. Crystals were obtained using polyethylene glycol 6000 as a precipitant and grew to 0.6 mm in the maximum dimension. The enzyme crystallized in the space group P2(1) with unit-cell dimensions a = 94.3, b = 117.0, and c = 114.2 A with beta = 109.2 degrees. Calculations indicate that there are four molecules in the asymmetric unit. The crystals diffract to at least 2.5 A resolution and the structure has been solved by molecular replacement using the lipase from Geotrichum candidum as a search model.

Structure of the Fab Fragment from a Neutralizing Monoclonal Antibody Directed Against an Epitope of gp41 from HIV-1

The structure of a Fab fragment of a monoclonal antibody (1583) that neutralizes a broad range of HIV-1 isolates has been solved by X-ray crystallography. This antibody is directed against a poliovirus/HIV-I chimaera which presents a conserved epitope of the envelope protein gp41. Crystals of 1583 were obtained in the space group P2(1)2(1)2(1) and the structure solved by molecular replacement. The model has been refined against all data in the range 10-2.9 A to a final crystallographic R factor of 0.198. The antigen-binding site features a well defined groove, typical of antibodies that bind to small antigens, created in part by a relatively short CDR H3. The variable regions of 1583 were sequenced and, given the hydrophilic nature of the epitope, revealed a surprising lack of charged residues in the CDR's. However, the antigen-binding cleft is indeed very polar, due in part to the presence of two charged residues that emanate from outside the recognized CDR's.

Structure of Diferric Duck Ovotransferrin at 2.35 Å Resolution

The structure of diferric duck ovotransferrin (DOT) has been determined and refined at a resolution of 2.35 A. The DOT structure, which contains two iron binding sites, is similar to the known transferrin and lactoferrin structures. The two iron-binding sites, one in the N-terminal lobe and one in the C-terminal lobe of the molecule, are similar but not identical. The main differences between the three known structures lie in the relative orientations of the N- and C-lobes with respect to each other. In the DOT structure the large aromatic side chain of Phe322 in the N-lobe packs against the conserved residue Gly387 in the C-lobe. This interaction is at the centre of the interface between the two lobes and could play a crucial role in determining their relative orientation. Other differences between the structures occur in the surface loops and in the peptide connecting the two lobes. The final crystallographic model consists of 5309 protein atoms (686 residues), two Fe(3+) ions, two (bi)carbonate ions and three carbohydrate moities. 318 water molecules have been added to the model. The final R factor is 0.22 for 25 400 observed reflections between 10 and 2.35 A resolution.

Crystallization and preliminary X-ray crystallographic data withEscherichia colitransketolase

The Escherichia coli enzyme transketolase, a dimeric protein of 2 x 70 kDa (662 amino acids) has been prepared from an overexpression system in E. coli. The purified enzyme has been crystallized from PIPES buffer pH 6.4 and ammonium sulfate. The crystals which grow as large plates diffract to greater than 1.9 A, resolution and are of the space group P2(1)2(1)2(1) with unit-cell dimensions of a = 74.6, b = 125.6 and c = 151.0 A, (Z = 8 with one transketolase dimer in the asymmetric unit). The structure has been solved by molecular replacement using the yeast transketolase enzyme structure as a search model. The enzyme is being used for large-scale biotransformations using various aldehydes and hydroxypyruvate as substrates.

Crystallization and preliminary X-ray analysis of a truncated tissue metalloproteinase inhibitor delta 128-194 TIMP-2

Crystals of an active truncated form of a human tissue metallproteinase inhibitor (delta 128-194 TIMP-2), a protein implicated in a number of diseases of the connective tissues, have been grown in a form suitable for study by X-ray diffraction analysis. Crystals grow using polyethylene glycol 600 as a precipitant and are in space group P2(1)2(1)2, with cell dimensions a = 75.28 A, b = 100.77 A, c = 31.45 A. The asymmetric unit appears to contain two molecules of delta TIMP-2 with a Vm value of 2.3 A3/dalton. The crystals diffract to Bragg-spacings beyond 2.5 A. Native data to 3.2 A have been collected and a search for heavy-metal derivatives is in progress.

Preliminary crystallographic studies on duck ovotransferrin

Crystals of duck ovotransferrin and duck apo-ovotransferrin have been grown from polyethylene glycol solutions. For both crystals, the space group is P2(1)2(1)2(1), the unit cell dimensions for the ovotransferrin are a = 49.6 A, b = 85.6 A, c = 178.7 A and for the apo-ovotransferrin a = 77.6 A, b = 98.8 A, c = 127.0 A, giving four molecules in the unit cell.