Masao Kakudo

Refined structure of cytochrome c3 at 1.8 Å resolution

The structure of cytochrome c3 from the sulfate-reducing bacterium Desulfovibrio vulgaris Miyazaki has been successfully refined at 1.8 A resolution. The crystallographic R factor is 0.176 for 9907 significant reflections. The isotropic temperature factors of individual atoms were refined and a total of 47 water molecules located on the difference map were incorporated in the refinement. The four heme groups are closely packed, with adjacent pairs of heme planes being nearly perpendicular to each other. The fifth and the sixth ligands of the heme iron atoms are histidine residues with N epsilon 2-Fe distances ranging from 1.88 A to 2.12 A. The histidine co-ordination to the heme iron is different for each heme group. The heme groups are all highly exposed to solvent, although the actual regions exposed differ among the hemes. The four heme groups are located in different environments, and the heme planes are deformed from planarity. The differences in the heme structures and their environments indicate that the four heme groups are non-equivalent. The chemical as well as the physical properties of cytochrome c3 should be interpreted in terms of the structural non-equivalence of the heme groups. The characteristic secondary structural non-equivalence of the heme groups. The characteristic secondary structures of the polypeptide chain of this molecule are three short alpha-helices, two short beta-strands and ten reverse turns.

Crystal and molecular structure of a collagen-like polypeptide (Pro-Pro-Gly)10☆

Abstract (Pro-Pro-Gly)10 forms single crystals, providing X-ray diffraction data to 0.22 nm resolution. In the crystals, the polypeptides form triplexes that aggregate end-to-end in quasi-infinite helices with axial translation per tripeptide h = 0.287 nm and the corresponding rotation t = −102.9 °. The structure, which may be an allomorph of collagen, has been refined by the linked-atom least-squares procedure. In addition, three water molecules per tripeptide have been detected by Fourier difference syntheses. One of them forms an intrachain hydrogen-bonded bridge O(Pro2) - - - W - - - O(Gly). There are also interchain hydrogen bonds (Gly)NH - - - O(Pro1) within the triplex.

Structure of rice ferricytochrome c at 2·0 Å resolution

The crystal structure of ferricytochrome c from rice embryos has been solved by X-ray diffraction to a resolution of 2.0 A, applying a single isomorphous replacement method with anomalous scattering effects. The initial molecular model was built on a graphics display system and was refined by the Hendrickson and Konnert method. The R factor was reduced to 0.25. Rice cytochrome c consists of III amino acid residues. In comparison with animal cytochromes c, the peptide chain extends for eight residues at the N-terminal end, which is characteristic for plant cytochromes c. These additional residues display a collagen-like conformation and an irregular reverse turn, and are located around the C-terminal alpha-helix on the surface or the rear side of the molecule. Two hydrogen bonds between the carbonyl oxygen of the N-terminal acetyl group and O eta of Tyr65, and between the peptide carbonyl oxygen of Pro-1 and O epsilon 1 of Gln89, are involved in holding these eight residues on the molecular surface, where Tyr65 and Gln89 are invariant in plant cytochromes c. Except for the extra eight residues, the main-chain conformations of both rice and tuna cytochromes c are essentially identical, though small local conformational differences are found at residues 24, 25, 56 and 57.

An X-ray study of the synthetic polypeptide (Pro-Pro-Gly)10

Abstract A polypeptide, (Pro-Pro-Gly) 10 , synthesized as a collagen model, gave a single crystal suitable for X-ray analysis with unit cell dimensions a = 26.9, b = 26.4, c = 100.4 A , and space group P 2 1 2 1 2 1 . The unit cell consists of four triple helices, whose locations are indicated on a tentative electron-density projection along the fiber axis. The helical parameters obtained from the three-dimensional intensity distribution and Patterson maps are: major helix radius 2.8 A; major helix pitch 60.24 A; vertical distance (parallel to c axis) between residues 2.87 A; number of residues in the repeat distance 21; and number of turns of minor helix in the repeat distance 7.

The crystal structure of the polymerization catalyst of acetaldehyde and its derivatives I. The crystal structure of dimethylaluminum N-phenylbenzimidate dimer, [(CH3)2AlOC(6H5)N(C6H5)]2

Abstract The crystal structure and molecular configuration of the highly stereospecific polymerization catalyst of acetaldehyde, dimethylaluminum N-phenylbenzimidate dimer, [(CH3)2AlOC(C6H5)N(C6H5)]2 have been determined from three-dimensional X-ray data collected photographically. The crystal belongs to the monoclinic system, space group P21/c, with two dimer formula units in a cell of dimensions: a=6.64±0.03, b=12.05±0.01, c=18.28±0.01 A, and β=94.9±0.02°. The structure has been refined by block-diagonal least-squares using anisotropic temperature factors for the nonhydrogen atoms. Hydrogen atoms with isotropic temperature factors were also included in the refinement. The final R index is 0.107 for 1096 non-zero reflections. The dimeric molecule is composed of a centro-symmetrical eight-membered ring; the aluminum atoms are bridged by OCN groups. The environmental of the aluminum atom is distorted tetrahedron: AlO = 1.805(6), AlN = 1.947(7), AlC = 1.940(11) and 1.940(11) A. The environments of the N and C atoms (of the eight-membered right) are trigonal. The configuration of the two adjacent benzene rings about the NC bond is cis.

The crystal structure of tert-butyloxycarbonyl-l-prolyl-l-leucylglycine hydrate

Enraf-Nonius Structure Determination Package (1975). Manual edited by B. FRENZ & Y. OKAVA. Molecular Structure Corporation, College Station, Texas, USA. JOHNSON, C. K. (1976). ORTEP II. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee. PRZYBYLSKA, M. (1974). Acta Cryst. B30, 2455-2459. SPEAKMAN, J. C. (1967). Chem. Commun. pp. 32-33. SRIVASTAVA, S. N. • PRZYBYLSKA, M. (1969). Acta Cryst. B25, 1651-1658. StrrroN, L. E. (1965). Tables of Interatomic Distances and Configuration in Molecules and Ions. London: The Chemical Society.

Crystal and molecular structure of the oxygen adduct, [Pt(O2)(PPh3)2],1·5 C6H6

The molecular structure of [Pt(O2)(PPh3)2] and the co-ordination of the O2 molecule to the Pt atom have been determined by the X-ray structure analysis of [Pt(O2)(PPh3)2], 1·5 C6H6.

Molecular Structure of p-Bromocarbobenzoxy-Glycyl-l-Prolyl-l-Leucyl-Glycine

WE have studied by X-ray analysis a series of oligopeptides, such as carbobenzoxy-Gly-Pro(OH), carbobenzoxy-Gly-Pro-Leu(OH), carbobenzoxy-Gly-Pro-Leu-Gly(OH) and carbobenzoxy-Gly-Pro-Leu-Gly-Pro(OH), which were prepared in order to examine the relationship between the structure of collagen and the substrate specificity for the enzyme reaction, of collagenase, and have already reported some of the results1–3. Recently, the three-dimensional analysis of the tetrapeptide, p-bromoearbo-benzoxy-Gly-Pro-Leu-Gly(OH), has been almost completed and a unique conformation was found in its structure.

Preliminary X-ray diffraction studies on a [4Fe4S] ferredoxin from Bacillus thermoproteolyticus

Abstract A [4Fe4S] ferredoxin from Bacillus thermoproteolyticus has been crystallized. The space group is P1 with two molecules in the unit cell, with the dimensions a = 32.96 A , b = 37.83 A , c = 39.82 A , α = 118.1 °, β = 104.2 ° and γ = 89.7 ° . The Bijvoet-difference Patterson map of the native crystal shows up a prominent peak of [4Fe4S] cluster.

The crystal structure of two forms of 1-ethyl-5-bromouracil

Abstract The molecular structure of 1-ethyl-5-bromouracil is studied by x-ray diffraction technique. 1-ethyl-5-bromouracil is crystallized in two forms, the form I with space group P21/c, and the form II with P42/n. The main structural difference between I and II is in the mode of hydrogen bond scheme joining uracil residues together in paris.