摘要:

The crystal structure of the DNA hexamer d(TGATCA) complexed with the anthracycline antibiotic idarubicin has been determined at 1.6 Å resolution. The asymmetric unit consists of a single hexamer oligonucleotide strand, one drug molecule and 35 water molecules. The complex crystallizes in the tetragonal space groupP41212,Z= 8 with lattice dimensions ofa=b= 28.19 (3),c= 52.77 (4) Å,V= 41 935 A3. The structure is isomorphous with a series of hexamer–anthracycline complexes and was solved by molecular replacement. Restrained least‐squares methods interspersed with computer‐graphics map inspection and model manipulation were used to refine the structure. TheRfactor is 0.22 for 2032 reflections withF≥ 3σ(F) in the resolution range 8.0–1.6 Å. The self‐complementary DNA forms a distorted B‐DNA double helix with two idarubicin molecules intercalated in the d(TpG) steps of the duplex. The duplex is formed by utilization of a crystallographic twofold axis of symmetry. The idarubicin chromophore is oriented at right angles to the long axis of the DNA base pairs with the anthracycline amino‐sugar moiety positioned in the minor groove. Our structure determination allows for comparison with a d(CGATCG)–idarubicin complex recently reported. Despite the sequence alteration at the intercalation step, the structures are very similar. The geometry of the intercalation and the nature of the interactions are conserved irrespective of the D

ISSN:1399-0047    

DOI:10.1107/S0907444992009983

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

The structure of the serine protease trypsin from the North Atlantic salmon (Salmo salar) has been solved by molecular replacement and refined by restrained least‐squares methods to a conventionalRfactor of 16.4% using diffractometer data in the 6.0–1.82 Å resolution range (14 443 reflections greater than 3σ). The model comprises 1793 protein atoms and 180 solvent molecules which were given unit occupancies, and the average temperature factors for protein atoms and solvent oxygen atoms are 15.2 and 36.8 Å2, respectively. The estimated error in atomic positions is about 0.2 Å. The structure of salmon trypsin was solved and refined with only a small part of the amino‐acid sequence known. However, a gene sequence of salmon trypsin has later become available. Some discrepancies between this sequence and the sequence obtained from the present X‐ray crystal study indicate that the mentioned sequences may correspond to isoenzymes. The structure of salmon trypsin is similar to other trypsins

ISSN:1399-0047    

DOI:10.1107/S0907444992013118

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

The structure of apo‐azurin fromAlcaligenes denitrificanshas been determined at high resolution by X‐ray crystallography. Two separate structure analyses have been carried out, (i) on crystals obtained from solutions of apo‐azurin and (ii) on crystals obtained by removal of copper from previously formed crystals of holo‐azurin. Data to 1.8 Å resolution were collected from the apo‐azurin crystals, by Weissenberg photography (with image plates) using synchrotron radiation and by diffractometry, and the structure was refined by restrained least‐squares methods to a finalRvalue of 0.160 for all data in the range 10.0–1.8 Å. The final model of 1954 protein atoms, 246 water molecules (66 half‐weighted), four SO42−ions, and two low‐occupancy (0.13 and 0.15) Cu atoms has r.m.s. deviations of 0.012, 0.045 and 0.013 Å from standard bond lengths, angle distances and planar groups. For copper‐removed azurin, data to 2.2 Å were collected by diffractometry and the structure refined by restrained least squares to a finalRvalue of 0.158 for all data in the range 10.0–2.2 Å. The final model of 1954 protein atoms, 264 water molecules, two SO42−ions, two low occupancy (0.18 and 0.22) metal atoms and one unidentified atom (modelled as S) has r.m.s. deviations of 0.013, 0.047 and 0.012 Å from standard bond lengths, angle distances and planar groups. The two structures are essentially identical to each other and show no significant differences from the oxidized and reduced holo‐azurin structures. The ligand side chains move slightly closer together following the removal of copper, with the radius of the cavity between the three strongly binding ligands, His 46, His 117 and Cys 112, shrinking from 1.31 Å in reduced azurin to 1.24 Å in oxidized azurin and 1.16 Å in apo‐azurin. There is a suggestion of increased flexibility in one of the copper‐binding loops but the structure supports the view that the copper site found in holo‐azurin is a stable structure, defined by the constraints of

ISSN:1399-0047    

DOI:10.1107/S0907444992013544

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

The crystal structure of prolyl‐glutaminyl‐valyl‐statyl‐alanyl‐leucine (Pro‐Gln‐Val‐Sta‐Ala‐Leu, C32H57N709.5H20,Mr= 683.9 + 90.1), a putative HTLV‐1 protease inhibitor based on one of the consensus retroviral protease cleavage sequences, and containing the statine residue [(4S,3S)‐4‐amino‐3‐hydroxy‐6‐methylheptanoic acid], has been determined by X‐ray diffraction. The same molecule has been modelled in the active site of the HTLV‐1 protease and both conformations have been compared. The peptide crystallizes as a pentahydrate in space groupP21witha= 10.874(2),b= 9.501(2),c= 21.062(5) Å, β = 103.68 (1)°,Z= 2,V= 2114.3 Å3,Dx= 1.21 g cm−3, μ = 8.02 cm−1,T= 293 K, λ(Cu Kα) = 1.5418 Å. The structure has been refined to anRvalue of 0.070 for 2152 observed reflections. The peptide main chain can be described as extended and adopts the usual zigzag conformation from the prolyl to the statyl residue. The main difference in conformation between the individual observed and modelled molecules is located on the Sta, Ala and Leu residues with the main chain of the modelled molecule rotated by about

ISSN:1399-0047    

DOI:10.1107/S0907444992013623

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

Aqualysin I, a thermostable protease found in the culture medium ofThermus aquaticusYT‐1, has been purified to homogeneity using a combination of ion‐exchange and affinity chromatography. It is a polypeptide with a molecular weight of 28 350 [Kwon, Terada, Matsuzawa&Ohta (1988).Eur. J. Biochem.173, 491–497] and is most active at 343–353 K and pH about 10.0 [Matsuzawa, Tokugawa, Hamaoki, Mizoguchi, Taguchi, Terada, Kwon&Ohta (1988).Eur. J. Biochem.171, 441–447]. Crystals of the enzyme are monoclinic, space groupP21, with cell dimensionsa= 40.80 (5),b= 64.39 (6),c= 45.51 (6) Å and β = 109.1 (1)°. The asymmetric unit consists of a single molecule (Vm= 1.99 Å3Da−1). The crystals are stable to X‐radiation and sca

ISSN:1399-0047    

DOI:10.1107/S0907444992012083

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

The fungalHumicola lanuginosalipase complexed with the inhibitorn‐dodecylphosphonate ethyl ester was crystallized in space groupP212121with pseudotetragonal unit‐cell parameters ofa= 131.7 (2),b= 131.3 (1),c= 75.4 (1) Å. 92% of X‐ray diffraction data to 2.8 Å resolution were collected with a finalRmerge= 8.5%. The crystals were grown using a new kind of precipitant – polyethylene glycol monomethyl ether (Peg‐mme) of

ISSN:1399-0047    

DOI:10.1107/S0907444993000952

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

ISSN:1399-0047    

DOI:10.1107/S0907444992013234

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

. A mutant (Serl39Ala) of the mouse recombinant catalytic (C) subunit of cAMP‐dependent protein kinase was co‐crystallized with a peptide inhibitor, PKI(5–24), and MEGA‐8 (octanoyl‐N‐methylglucamide) detergent. This structure was refined using all observed data (30 248 reflections) between 30 and 1.95 Å resolution to anRfactor of 0.186. R.m.s. deviations of bond lengths and bond angles are 0.013 Å and 2.3°, respectively. The final model has 3075 atoms (207 solvent) with a meanBfactor of 31.9 Å2. The placement of invariant protein‐kinase residues and mostC:PKI(5–24) interactions were confirmed, but register errors affecting residues 55–64 and 309–339 were corrected during refinement by shifting the affected sequences toward the C terminus along the previously determined backbone path. New details ofC:PKI(5–24) interactions and the Ser338 autophosphorylation site are described, and the acyl group binding site near the catalytic

ISSN:1399-0047    

DOI:10.1107/S0907444993000502

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

. The crystal structure of a ternary complex containing the catalytic subunit of cAMP‐dependent protein kinase, ATP and a 20‐residue inhibitor peptide was refined at a resolution of 2.2 Å to anRvalue of 0.177. In order to identify the metal binding sites, the crystals, originally grown in the presence of low concentrations of Mg2+, were soaked in Mn2+. Two Mn2+ions were identified using an anomalous Fourier map. One Mn2+ion bridges the γ‐ and β‐phosphates and interacts with Asp184 and two water molecules. The second Mn2+ion interacts with the side chains of Asn171 and Asp l84 as well as with a water molecule. Modeling a serine into the P site of the inhibitor peptide suggests a mechanism for pho

ISSN:1399-0047    

DOI:10.1107/S0907444993000423

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY