Structure of hexagonal turkey egg-white lysozyme at 1.65Å resolution

The structure of a monoclinic form of bovine pancreatic trypsin inhibitor (BPTI) crystallized from a thiocyanate solution has been determined and re®ned at 2.7 A Ê resolution. The space group is P2 1 with a = 71.56, b = 73.83, c = 64.47 A Ê , = 93.9and Z = 20. The ten independent molecules were located by a multi-body molecular-replacement search as developed in the AMoRe program, starting from a single monomer model (PDB code: 6PTI). The molecular arrangement of the subunits is a decamer resulting from the combination of two orthogonal ®vefold and twofold noncrystallographic axes. This builds a globular micelle-like particle which minimizes hydrophobic interactions with the solvent. The re®nement was conducted with non-crystallographic symmetry constraints up to a ®nal residual of R = 0.20 (R free = 0.26). The root-mean-square deviations from ideal geometry were 0.015 A Ê and 1.6 on bond distances and bond angles, respectively. Several sites for thiocyanate ions were analyzed.

Section: The Thiocyanate Ions and Their Role In Decamer Buildingsupporting

confidence: 64%

Section: Introductionmentioning

confidence: 99%

The decameric structure of bovine pancreatic trypsin inhibitor (BPTI) crystallized from thiocyanate at 2.7 Å resolution

Hamiaux

Prangé

Riès-Kautt

et al. 1999

“…References for the lysozyme structures we have used are as follows: hen egg-white lysozyme, 5lym (Rao & Sundaralingam, 1996), 2lzt (Ramanadham et al, 1990), 193l and194l (Vaney et al, 1996), 1lkr, 1lks (Steinrauf, 1998), 3lzt and 4lzt (Walsh et al, 1998), 1azf (Lim et al, 1998), 1lz8 and 1lz9 ; turkey egg-white lysozyme, 1tew (Howell, 1995); bob quail egg-white lysozyme, 1dkk (Chacko et al, 1996); human lysozyme, 1jka, 1jkb, 1jkc and 1jkd (Muraki et al, 1997), 1lmt (Yamada et al, 1995), 1lz5 and 1lz6 (Yamada et al, 1993) and 1lzr (Song et al, 1994). Other coordinates, kindly provided by their authors, were included in the list: water molecules and nitrate ions for the human lysozyme structure (1lz1) at 1.5 A Ê resolution (Blake et al, 1983), two hen eggwhite lysozyme structures complexed with neutral bromophenol red (BPR) and with neutral bromophenol blue (BPB) (Madhusudan & Vijayan, 1992) and three sets of HEWL coordinates studied using neutron diffraction: 1lzn (Bon et al, 1999), crystallized in dimethyl sulfoxide (Lehmann et al, 1985) and in ethanol (Lehmann & Stans®eld, 1989).…”

Section: Structure Comparisonsmentioning

confidence: 99%

Structural effects of monovalent anions on polymorphic lysozyme crystals

Vaney¹,

Broutin²,

Retailleau³

et al. 2001

112

Understanding direct salt effects on protein crystal polymorphism is addressed by comparing different crystal forms (triclinic, monoclinic, tetragonal and orthorhombic) for hen, turkey, bob white quail and human lysozymes. Four new structures of hen egg‐white lysozyme are reported: crystals grown in the presence of NapTS diffracted to 1.85 Å, of NaI to 1.6 Å, of NaNO3 to 1.45 Å and of KSCN to 1.63 Å. These new structures are compared with previously published structures in order to draw a mapping of the surface of different lysozymes interacting with monovalent anions, such as nitrate, chloride, iodide, bromide and thiocyanate. An analysis of the structural sites of these anions in the various lysozyme structures is presented. This study shows common anion sites whatever the crystal form and the chemical nature of anions, while others seem specific to a given geometry and a particular charge environment induced by the crystal packing.

“…The restrained least-squares procedure has been described in further detail elsewere (Von Dreele, 2005). Furthermore, to test the validity of the final model, refinements were carried out starting from each of the possible models [1tew (Howell, 1995), 3lz2 (Howell et al, 1992), 2lz2 (Parsons & Phillips, unpublished work)]. Refinements involving 1tew converged to better final R values than those using 2lz2 and 3lz2, suggesting that the refinement was also sensitive to the initial model used.…”

Section: Molecular Structurementioning

confidence: 99%

“…Currently, there are four entries in the PDB for hexagonal TEWL, spanning a pH range of 4.5-8 [PDB codes 1lz2 (Sarma & Bott, 1977), 2lz2 (Parsons & Phillips, unpublished work), 3lz2 (Howell et al, 1992) and 1tew (Howell, 1995)]. The space group (P6 1 22) has not been previously reported for HEWL.…”

Section: Introductionmentioning

confidence: 99%

Synchrotron X-ray powder diffraction study of hexagonal turkey egg-white lysozyme

Margiolaki

Wright

Fitch

et al. 2005

The structure of turkey egg-white lysozyme (TEWL) has been refined from high-resolution X-ray powder diffraction data. The sample was rapidly obtained as a polycrystalline precipitate at high protein concentration using 0.5 M NaCl solvent pH 6 and was deposited in the PDB with code 1xft. The diffraction data were collected at room temperature. Molecular replacement was shown to give a suitable starting point for refinement, illustrating that powder data can be sufficient for this approach. Crystallographic models were then refined by combined Rietveld and stereochemical restraint analysis of the powder data (d(min) = 3.35 A), resulting in the extraction of reliable lattice parameters and the refinement of the molecular conformation at room temperature. The structure is hexagonal [space group P6(1)22, unit-cell parameters a = 71.0862 (3), c = 85.0276 (5) A] with 12 symmetry-related molecules in the unit cell, in agreement with previous studies. The results of our analysis are indicative of specific amino acids being disordered at this temperature. Upon cooling, a sudden drop in the lattice parameters at approximately 250 K is observed concurrently with the freezing of the mother liquor. The observation of severe peak broadening below this temperature indicates strain effects accompanying the freezing transition, which are found to be reversible. Finally, a correlation between the unit-cell parameters and the pH of the buffer solution is evident, in a similar manner to earlier observations on HEWL.