1WTM

X-ray structure of HEW Lysozyme Orthorhombic Crystal formed in the Earth's magnetic field

Summary for 1WTM

• Entry DOI: 10.2210/pdb1wtm/pdb
• Related: 1BGI 1WTN
• Descriptor: Lysozyme C, CHLORIDE ION (3 entities in total)
• Functional Keywords: allergen, hydrolase
• Biological source: Gallus gallus (chicken)
• Cellular location: Secreted: P00698
• Total number of polymer chains: 1
• Total formula weight: 14366.61

Authors

Saijo, S.,Yamada, Y.,Sato, T.,Tanaka, N.,Matsui, T.,Sazaki, G.,Nakajima, K.,Matsuura, Y. (deposition date: 2004-11-25, release date: 2004-12-14, Last modification date: 2024-10-30)

Primary citation

Saijo, S.,Yamada, Y.,Sato, T.,Tanaka, N.,Matsui, T.,Sazaki, G.,Nakajima, K.,Matsuura, Y.
Structural consequences of hen egg-white lysozyme orthorhombic crystal growth in a high magnetic field: validation of X-ray diffraction intensity, conformational energy searching and quantitative analysis of B factors and mosaicity.
Acta Crystallogr.,Sect.D, 61:207-217, 2005

PubMed Abstract: A novel method has been developed to improve protein-crystal perfection during crystallization in a high magnetic field and structural studies have been undertaken. The three-dimensional structure of orthorhombic hen egg-white (HEW) lysozyme crystals grown in a homogeneous and static magnetic field of 10 T has been determined and refined to a resolution of 1.13 angstroms and an R factor of 17.0%. The 10 T crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 56.54 (3), b = 73.86 (6), c = 30.50 (2) angstroms and one molecule per asymmetric unit. A comparison of the structures of the 0 T and 10 T crystals has been carried out. The magnitude of the structural changes, with a root-mean-square deviation value of 0.75 angstroms for the positions of all protein atoms, is similar to that observed when an identical protein structure is resolved in two different crystalline lattices. The structures remain similar, with the exception of a few residues e.g. Arg68, Arg73, Arg128 and Gln121. The shifts of the arginine residues result in very significant structural fluctuations, which can have large effects on a protein's crystallization properties. The high magnetic field contributed to an improvement in diffraction intensity by (i) the displacement of the charged side chains of Arg68 and Arg73 in the flexible loop and of Arg128 at the C-terminus and (ii) the removal of the alternate conformations of the charged side chains of Arg21, Lys97 or Arg114. The improvement in crystal perfection might arise from the magnetic effect on molecular orientation without structural change and differences in molecular interactions. X-ray diffraction and molecular-modelling studies of lysozyme crystals grown in a 10 T field have indicated that the field contributes to the stability of the dihedral angle. The average difference in conformational energy has a value of -578 kJ mol(-1) per charged residue in favour of the crystal grown in the magnetic field. For most protein atoms, the average B factor in the 10 T crystal shows an improvement of 1.8 angstroms(2) over that for the 0 T control; subsequently, the difference in diffraction intensity between the 10 T and 0 T crystals corresponds to an increase of 22.6% at the resolution limit. The mosaicity of the 10 T crystal was better than that of the 0 T crystal. More highly isotropic values of 0.0065, 0.0049 and 0.0048 degrees were recorded along the a, b and c axes, respectively. Anisotropic mosaicity analysis indicated that crystal growth is most perfect in the direction that corresponds to the favoured growth direction of the crystal, and that the crystal grown in the magnetic field had domains that were three times the volume of those of the control crystal. Overall, the magnetic field has improved the quality of these crystals and the diffracted intensity has increased significantly with the magnetic field, leading to a higher resolution.

PubMed: 15735330
DOI: 10.1107/S0907444904030926

Experimental method

X-RAY DIFFRACTION (1.33 Å)