Structure of myohemerythrin in the azidomet state at 1.71. 3Å resolution

S Sheriff, WA Hendrickson, JL Smith - Journal of molecular biology, 1987 - Elsevier
S Sheriff, WA Hendrickson, JL Smith
Journal of molecular biology, 1987Elsevier
The molecular model of myohemerythrin, an oxygen-carrying protein from sipunculan
worms, has been refined by stereochemically restrained least-squares minimization at 1.7
1.3 A ̊ resolution to a conventional R-value of 0.158. The estimated positional standard
deviation is better than 0.15 Å for most of the 979 protein atoms. The average isotropic
displacement parameter, B, for the protein atoms is 23.1 Å 2. This high average B parameter
appears to be due to the overall motion of the molecule, which correlates with the observed …
The molecular model of myohemerythrin, an oxygen-carrying protein from sipunculan worms, has been refined by stereochemically restrained least-squares minimization at 1.7 1.3 A ̊ resolution to a conventional R-value of 0.158. The estimated positional standard deviation is better than 0.15 Å for most of the 979 protein atoms. The average isotropic displacement parameter, B, for the protein atoms is 23.1 Å 2. This high average B parameter appears to be due to the overall motion of the molecule, which correlates with the observed anisotropic diffraction. The side-chains of seven residues were modeled in two conformations, ie the side-chains were discretely disordered, and B parameters for several lysine and glutamate side-chains indicate that they are poorly localized. Of the residues in myohemerythrin, 66% are helical, with 62% occurring in four long α-helices with mean values for the backbone torsion angles of φ=− 65°, gy=− 42°, and for the hydrogen bonds distances of N… O, 3.0 Å and H… O, 2.1 Å, and angles of N… Ô C, 153°, N Ĥ… O, 157°, and H… Ô C, 147°. For two-thirds of the α-helical residues, the torsional rotation of the C α C β bond, χ 1 approximately− 60°, and for one-third χ 1 approximately 180°. Although most turns in myohemerythrin are well-categorized by previous classification, two do not fit in established patterns. Also included in the refined model are three sulfate ions, all partially occupied, and 157 water molecules, 40% of which are modeled fully occupied. Only one water molecule is internal to the protein, the remainder occur on the surface and are observed principally between symmetry-related molecules contributing, along with van der Waals' contacts, most of the interactions between molecules. There are eight intermolecular protein-protein hydrogen bonds, of which only four are between welllocated atoms.
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