Date: Dec.1999
Mtx-Val-D-mLeu-(-Thr-bAla-D-Leu-mIle-bAla-D- alloIle-mVal-mAla-bAla-D-Leu-malloIle-), 13-water hydrates

Mtx=methoxyacetate, m=N-methyl, bAla=beta-alanine
Chemical scheme is here.

Left: Amphiphatic layer structure in the crystal. Colored balls represent the solvated water molecules and the arrows show the water-layers. Drawn radius is 35 A.
Abstract: Theonellapeptolide-Id (TNLP), a cyclic tridecapeptide lactone, was crystallized from dimethylformamide-water solution. In the asymmetric unit, two peptide molecules were existed with solvent molecules, and total molecular weight were over 3000 Dalton. The crystal structure including solvent molecules was finally determined at 0.80 A resolution by using synchrotron radiation. The conformations of two independent molecules were similar to each other and were also similar to the previously reported structure (Doi, Ishida, Kobayashi, Deschamps & Flippen-Anderson (1999) Acta Crystallogr., Sect. C, 55, 796-798). About thirteen hydrated waters were found at disordered nineteen sites, and they were located on a certain region to avoid the contacts with aliphatic side chains of peptolide in the crystal. The spatial dispositions of solvent molecules and peptides subsequently created the amphipathic layer structure. This unique behavior was elucidated by X-ray analysis as a noteworthy characteristic of TNLP-Id.
References of theonellapeptolide:
  1. Kobayashi, M., Lee, N. K., Shibuya, H., Momose, T. & Kitagawa, I. (1991) Chem. Pharm. Bull. 39, 1177-1184.
  2. Kobayashi, M., Kanzaki, K., Katayama, S., Ohashi, K., Okada, H., Ikegami, S. & Kitagawa, I. (1994) Chem. Pharm. Bull. 42, 1410-1415.
  3. Kobayashi, M., Kawazoe, K., Okamoto, T., Sasaki, T. & Kitagawa, I. (1994) Chem. Pharm. Bull. 42, 19-26.
  4. Kobayashi, J., Itagaki, F., Shigemori, H., Ishibashi, M., Takahashi, K., Ogura, M., Nagasawa, S., Nakamura, T., Hirota, H., Ohta, T. & Nozoe, S. (1991) J. Am. Chem. Soc. 113, 7812-7813.
  5. Kobayashi, M., Kawazoe, K., Katori, T. & Kitagawa, I. (1992) Chem. Pharm. Bull. 40, 1773-1778.
  6. Kitagawa, I., Lee, N.K., Kobayashi, M. & Shibuya, H. (1987) Chem. Pharm. Bull. 35, 2129-2132.
  7. Kitagawa, I., Lee, N.K., Kobayashi, M. & Shibuya, H. (1987) Tetrahedron, 47, 2169-2171.
  8. Doi, M., Ishida, T., Kobayashi, M., Deschamps, J. R. & Flippen-Anderson, J. L. (1999) Acta Crystallogr., Sect. C, 55, 796-798. (see orthorhombic [monomeric] structure)
  9. Bernardinelli, G., Jefford, C.W., Sakai, R. & Higa, T. (1992) Abstracts of Papers, 7th International Symposium on Marine Natural Products, p29-30, Capri, Italy.

ORTEP-III (Burnett, 1996) drawing of Molecule 1.

ORTEP-III (Burnett, 1996) drawing of Molecule 2.
The conformation of Molecules 1 & 2 are similar to each other except for N-terminus and some loop. The other feature is cis amide bond between Val and Ala (lower coner in the figure).

Side view of Molecule 1.
Main chain is thick line and fairely winded.

Side view of Molecule 2.
Shape is like as a "bottom of ship".

X-Ray Data Summary
formula2(C70H125N13O16), 12.9H2O
symmetry monoclinic
space group P21
Cell Crystal
a 11.9955(3) Ang. description block
b 36.9917(10) Ang. colour Colorless
c 19.7887(3) Ang. size (mm) 0.3x0.2x0.2
alpha 90.0 deg. Dx (g/ml) 1.069
beta 96.1623(15) deg. F(000) 3056
gamma 90.0 deg. mu(CuKa) 0.076
volume 8730.2(3) Ang^3 wave length0.834 A
Z 4 temperature100(2)
Diffrn measurementRefinementspace
device type Rigaku RAXIS-4 Flack 0.5(11)
radiation source SPring-8/BL24XU-A* parameters 2002
index limit 0~h~15, 0~k~46, -24~L~24 restraints 396
theta (deg.) 2.3-31.5 R_factor_gt 0.0865
total reflections 16300 wR_factor_gt 0.2492
reflections(obs) 14826 .gt. 2sigma(I) dela rho_max 0.802 e A^3
Structure delta rho_min -0.428 e A^3
solution SnB shift/su_max7.069
refinementSHELXL-97 Goodness of fit 1.111

*The machine time of the synchrotron was given from Hyogo prefecture and Japan Synchrotron Radiation Research Institute with the proposal No. C99A24XU-005N.


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