PDBsum entry: 1bgi

Hydrolase

PDB id: 1bgi

Contents

Protein chain

129 a.a. *

Metals

_CL

Waters ×109

* Residue conservation analysis

PDB id:

1bgi

Name:

Hydrolase

Title:

Orthorhombic lysozyme crystallized at high temperature (310k)

Structure:

Lysozyme. Chain: a. Other_details: orthorhombic crystal form

Source:

Gallus gallus. Chicken. Organism_taxid: 9031. Cell: egg. Cellular_location: cytoplasm (white)

Resolution:

1.70Å R-factor: 0.186 R-free: 0.216

Authors:

H.Oki,Y.Matsuura,H.Komatsu,A.A.Chernov

Key ref:

H.Oki et al. (1999). Refined structure of orthorhombic lysozyme crystallized at high temperature: correlation between morphology and intermolecular contacts. Acta Crystallogr D Biol Crystallogr, 55, 114-121. PubMed id: 10089401 DOI: 10.1107/S0907444998008713

Date:

28-May-98 Release date: 28-Oct-98

Protein chain

P00698  (LYSC_CHICK) -  Lysozyme C

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.

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (2 terms)
• Biological process: metabolic process (4 terms)
• Biochemical function: catalytic activity (5 terms)

DOI no: 10.1107/S0907444998008713

Acta Crystallogr D Biol Crystallogr 55:114-121 (1999)

PubMed id: 10089401

Refined structure of orthorhombic lysozyme crystallized at high temperature: correlation between morphology and intermolecular contacts.

H.Oki, Y.Matsuura, H.Komatsu, A.A.Chernov.

ABSTRACT

The structure of orthorhombic hen egg-white lysozyme (HEWL) crystallized at 310 K has been refined at 1.7 A resolution. Large displacements of the side-chain atoms with respect to the tetragonal structure were observed in many places, in contrast to small displacements of the main-chain atoms. A chloride-ion binding site was observed at an interface of two molecules, but at a different position to the binding site in the tetragonal form. The analysis of intermolecular contacts in the crystal has shown the presence of three independent intermolecular contacts which are called macrobonds A, B and C. Arginine side chains are frequently involved in these macrobonds, suggesting that the high frequency of this residue in HEWL may be a possible reason for the multiple polymorphs of this protein. The crystal forms were determined using a light-reflecting device on a four-circle diffractometer. Correlations between crystal forms and the three-dimensional macrobond networks were interpreted in terms of their components in various crystallographic planes, making use of approximate strengths of hydrogen-bond and van der Waals interatomic forces.

Selected figure(s)

Figure 3.
Figure 3 Appearances of the contacts of the two molecules via (a) macrobond A, (b) macrobond B and (c) macrobond C. A yellow sphere in (a) shows the bound chloride ion.

Figure 7.
Figure 7 A stereoscopic view of macrobond chains in the orthorhombic crystal. The macrobonds A, B and C are shown as red, yellow and blue lines, respectively, connecting the contact site and the centre of molecules. V^across(hkl) was derived by studying this picture from various directions by rotation of the computer graphics.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1999, 55, 114-121) copyright 1999.

Figures were selected by the author.