PDBsum entry 1gwd

Lysozyme

PDB id: 1gwd

Contents

Protein chain

129 a.a. *

Ligands

EDO ×2

CMO

Metals

IOD ×5

_CL ×7

_NA ×3

Waters ×103

* Residue conservation analysis

PDB id:

1gwd

Name:

Lysozyme

Title:

Tri-iodide derivative of hen egg-white lysozyme

Structure:

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

Source:

Gallus gallus. Chicken. Organism_taxid: 9031

Biol. unit:

Monomer (from PDB file)

Resolution:

1.77Å R-factor: 0.170 R-free: 0.211

Authors:

G.Evans,G.Bricogne

Key ref:

G.Evans and G.Bricogne (2002). Triiodide derivatization and combinatorial counter-ion replacement: two methods for enhancing phasing signal using laboratory Cu Kalpha X-ray equipment. Acta Crystallogr D Biol Crystallogr, 58, 976-991. PubMed id: 12037300 DOI: 10.1107/S0907444902005486

Date:

14-Mar-02 Release date: 06-Jun-02

Protein chain

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.

DOI no: 10.1107/S0907444902005486

Acta Crystallogr D Biol Crystallogr 58:976-991 (2002)

PubMed id: 12037300

Triiodide derivatization and combinatorial counter-ion replacement: two methods for enhancing phasing signal using laboratory Cu Kalpha X-ray equipment.

G.Evans, G.Bricogne.

ABSTRACT

A series of experiments performed at Cu Kalpha wavelength on in-house X-ray equipment are presented which investigate two possibilities for enhancing the experimental phasing signal by means of (i) triiodide/iodide soaks using KI/I(2) and (ii) combinations of counter-ions introduced using the short cryosoak method. Triiodide-derivative crystal structures for five test proteins have been refined and reveal that iodine can bind as polyiodide and single iodide ions through hydrophobic and hydrogen-bonding interactions both at the molecular surface and in intramolecular and intermolecular cavities. In three cases, the structures could be automatically determined with autoSHARP using in-house SAD and SIRAS data. The investigation of combinatorial counter-ion replacement using multiple salts with Na(+) and Cs(+) as cations and I(-) and Cl(-) as anions reveals that, for the case of hen egg-white lysozyme, significant improvement in phasing signal is obtained by the combined use of salts compared with SIRAS methods using native and single short-soak derivative data sets.

Selected figure(s)

Figure 2.
Figure 2 Region of the elastase molecule showing the common binding site for (a) iodine and (b) xenon.

Figure 6.
Figure 6 Example of a pentaiodide molecule (sites B21-B25) binding in a partially solvent-exposed pocket formed between two symmetry-related molecules of XI. The pentaiodide is tethered at each end by hydrogen bonds (yellow dashes) formed with Gln234 NE2 and Lys240 NZ. The central three atoms contact through van der Waals interactions. The symmetry-related protein molecule is shown in green. The anomalous difference Fourier map contoured at 4 is shown in red mesh.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 976-991) copyright 2002.

Figures were selected by an automated process.