PDBsum entry 5o4x

Hydrolase

PDB id: 5o4x

Contents

Protein chains

129 a.a.

PDB id:

5o4x

Name:

Hydrolase

Title:

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal

Structure:

LysozymE C. Chain: a, b. Synonym: 1,4-beta-n-acetylmuramidasE C,allergen gal d iv. Ec: 3.2.1.17

Source:

Gallus gallus. Chicken. Organism_taxid: 9031

Authors:

M.T.B.Clabbers,E.Van Genderen,W.Wan,E.L.Wiegers,T.Gruene,J.P.Abrahams

Key ref:

M.T.B.Clabbers et al. (2017). Protein structure determination by electron diffraction using a single three-dimensional nanocrystal. Acta Crystallogr D Struct Biol, 73, 738-748. PubMed id: 28876237

Date:

31-May-17 Release date: 23-Aug-17

Protein chains

P00698  (LYSC_CHICK) -  Lysozyme C from Gallus gallus

Seq: 147 a.a.

Struc: 129 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.17 - lysozyme.
• Reaction: Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.

Acta Crystallogr D Struct Biol 73:738-748 (2017)

PubMed id: 28876237

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal.

M.T.B.Clabbers, E.van Genderen, W.Wan, E.L.Wiegers, T.Gruene, J.P.Abrahams.

ABSTRACT

Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm³, i.e. no more than 6 × 10⁵unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures.