Monoclinic HEWL derivative structure at 0.75 Å resolution

Tris-dipicolinate lanthanide complex, Na3.[Ln(DPA)3], where DPA stands for pyridine-2,6 dicarboxylate, has been proven to be especially interesting to produce derivative crystals with high phasing power [1]. The lanthanide complex can act as a cross-linking agent, which binds at the interface between protein molecules, leading to a supramolecular interaction at the crystal scale [2]. In the case of hen egg-white lysozyme (HEWL), derivative crystals obtained by co-crystallization with Yb(DPA)33-belong to the space group C2, in similar crystallization conditions that normally lead to the tetragonal form P43212. Data were collected on a derivative crystal up to a resolution of 0.75 Å at the EMBL beamline P13 at PETRA III at DESY (Hamburg, Germany). Taking advantage of the high the resolution and the strong anomalous signal of the Yb3+(f″ = 5.2 e-at 17 keV), the structure was solved by both SAD and ab initio methods. Data collection, experimentally phased electron density maps and the structure, especially with respect to the vicinity of the lanthanide binding sites, will be discussed.

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The binding of platinum hexahalides (Cl, Br and I) to hen egg-white lysozyme and the chemical transformation of the PtI6octahedral complex to a PtI3moiety bound to His15

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x14014009 ◽

2014 ◽

Vol 70 (9) ◽

pp. 1132-1134 ◽

Cited By ~ 7

Author(s):

Simon W. M. Tanley ◽

Laurina-Victoria Starkey ◽

Lucinda Lamplough ◽

Surasek Kaenket ◽

John R. Helliwell

Keyword(s):

Heavy Atom ◽

Egg White ◽

Hen Egg White Lysozyme ◽

Egg White Lysozyme ◽

Density Maps ◽

Square Planar ◽

Chemical Behaviour ◽

Hen Egg White ◽

Derivatives Of ◽

Hen Egg

This study examines the binding and chemical stability of the platinum hexahalides K2PtCl6, K2PtBr6and K2PtI6when soaked into pre-grown hen egg-white lysozyme (HEWL) crystals as the protein host. Direct comparison of the iodo complex with the chloro and bromo complexes shows that the iodo complex is partly chemically transformed to a square-planar PtI3complex bound to the Nδatom of His15, a chemical behaviour that is not exhibited by the chloro or bromo complexes. Each complex does, however, bind to HEWL in its octahedral form either at one site (PtI6) or at two sites (PtBr6and PtCl6). As heavy-atom derivatives of a protein, the octahedral shape of the hexahalides could be helpful in cases of difficult-to-interpret electron-density maps as they would be recognisable `objects'.

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Feasibility study for the measurement of a large set of triplet phases from a small protein

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444999005338 ◽

1999 ◽

Vol 55 (7) ◽

pp. 1320-1328 ◽

Cited By ~ 1

Author(s):

Edgar Weckert ◽

Kerstin Hölzer ◽

Klaus Schroer ◽

Johannes Zellner ◽

Kurt Hümmer

Keyword(s):

Experimental Data ◽

Egg White ◽

Large Set ◽

Hen Egg White Lysozyme ◽

Small Protein ◽

Egg White Lysozyme ◽

Small Proteins ◽

Tetragonal Form ◽

Hen Egg White ◽

Hen Egg

The feasibility of measuring a set of triplet phases large enough to solve the structure of a small protein has been evaluated. A total of about 850 triplet phases have been measured from the tetragonal form of hen egg-white lysozyme. From these triplet phases, about 750 single phases can be derived. The experimental details of these measurements as well as the results, the values of the measured triplet phases, are reported. Additional experimental data from other small proteins are also presented.

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Simplified heavy-atom derivatization of protein structures via co-crystallization with the MAD tetragon tetrabromoterephthalic acid

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x21004052 ◽

2021 ◽

Vol 77 (5) ◽

pp. 156-162

Author(s):

Jia Q. Truong ◽

Stephanie Nguyen ◽

John B. Bruning ◽

Keith E. Shearwin

Keyword(s):

Heavy Atom ◽

Protein Structures ◽

Molecular Replacement ◽

Hen Egg White Lysozyme ◽

Phase Problem ◽

Egg White Lysozyme ◽

Mad Phasing ◽

Experimental Phasing ◽

Anomalous Signal ◽

Hen Egg White

The phase problem is a persistent bottleneck that impedes the structure-determination pipeline and must be solved to obtain atomic resolution crystal structures of macromolecules. Although molecular replacement has become the predominant method of solving the phase problem, many scenarios still exist in which experimental phasing is needed. Here, a proof-of-concept study is presented that shows the efficacy of using tetrabromoterephthalic acid (B4C) as an experimental phasing compound. Incorporating B4C into the crystal lattice using co-crystallization, the crystal structure of hen egg-white lysozyme was solved using MAD phasing. The strong anomalous signal generated by its four Br atoms coupled with its compatibility with commonly used crystallization reagents render B4C an effective experimental phasing compound that can be used to overcome the phase problem.

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Modeling the Binding Sites of Anti-Hen Egg White Lysozyme Antibodies HyHEL-8 and HyHEL-26: An Insight into the Molecular Basis of Antibody Cross-Reactivity and Specificity

Biophysical Journal ◽

10.1016/s0006-3495(03)74740-7 ◽

2003 ◽

Vol 85 (5) ◽

pp. 3221-3236 ◽

Cited By ~ 22

Author(s):

S. Mohan ◽

Neeti Sinha ◽

Sandra J. Smith-Gill

Keyword(s):

Binding Sites ◽

Molecular Basis ◽

Egg White ◽

Cross Reactivity ◽

Hen Egg White Lysozyme ◽

Egg White Lysozyme ◽

Hen Egg White ◽

Insight Into ◽

Hen Egg

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An X-ray study of the physiological-temperature form of hen egg-white lysozyme at 2 Å resolution

Proceedings of the Royal Society of London Series B Biological Sciences ◽

10.1098/rspb.1983.0021 ◽

1983 ◽

Vol 217 (1209) ◽

pp. 471-489 ◽

Cited By ~ 29

Keyword(s):

High Temperature ◽

Egg White ◽

Hen Egg White Lysozyme ◽

Final Model ◽

Egg White Lysozyme ◽

Isomorphous Replacement ◽

Tetragonal Form ◽

Hen Egg White ◽

Mean Square Difference ◽

Hen Egg

The structure of the high-temperature orthorhombic form of hen egg-white lysozyme has been determined at 2.0 Å resolution. Initial images of the molecule were obtained at 6.0 Å resolution both by double isomorphous replacement and by molecular replacement with use of the known structure of the room-temperature tetragonal lysozyme. The initial model thus obtained ( R = 0.52 at 6.0 Å) was refined first as a rigid body at 6.0 Å and then by restrained least squares at 2.5 Å and later at 2.0 Å resolution. The final model ( R = 0.23 at 2.0 Å) was compared with that of the tetragonal form: the structures are very similar with a root mean square difference in superimposed α-carbon coordinates of 0.46 Å. There are, however, differences which are caused by a crystal contact involving the upper part of this active site in the high-temperature orthorhombic form. Because of this, residues Trp 62 and Pro 70 are much better ordered than in the tetragonal form, where they are exposed to solvent. These differences can partly explain the difficulty of inhibitor-binding in high-temperature orthorhombic crystals, but do not seem to reflect the particular behaviour of lysozyme in solution at high temperature.

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A dipicolinate lanthanide complex for solving protein structures using anomalous diffraction

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444910010954 ◽

2010 ◽

Vol 66 (7) ◽

pp. 762-769 ◽

Cited By ~ 15

Author(s):

Guillaume Pompidor ◽

Olivier Maury ◽

Jean Vicat ◽

Richard Kahn

Keyword(s):

Protein Structures ◽

Lanthanide Complex ◽

Egg White ◽

Urate Oxidase ◽

Anomalous Scattering ◽

X Rays ◽

Hen Egg White Lysozyme ◽

Egg White Lysozyme ◽

Hen Egg White ◽

Hen Egg

Tris-dipicolinate lanthanide complexes were used to prepare derivative crystals of six proteins: hen egg-white lysozyme, turkey egg-white lysozyme, thaumatin fromThaumatococcus daniellii, urate oxidase fromAspergillus flavus, porcine pancreatic elastase and xylanase fromTrichoderma reesei. Diffraction data were collected using either synchrotron radiation or X-rays from a laboratory source. In all cases, the complex turned out to be bound to the protein and the phases determined using the anomalous scattering of the lanthanide led to high-quality electron-density maps. The binding mode of the complex was characterized from the refined structures. The lanthanide tris-dipicolinate was found to bind through interactions between carboxylate groups of the dipicolinate ligands and hydrogen-bond donor groups of the protein. In each binding site, one enantiomeric form of the complex is selected from the racemic solution according to the specific site topology. For hen egg-white lysozyme and xylanase, derivative crystals obtained by cocrystallization belonged to a new monoclinicC2 crystal form that diffracted to high resolution.

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