PDBsum entry 2d6b

Hydrolase

PDB id: 2d6b

Contents

Protein chain

129 a.a. *

Ligands

202 ×9

Metals

_CL ×2

_NA

Waters ×298

* Residue conservation analysis

PDB id:

2d6b

Name:

Hydrolase

Title:

Novel bromate species trapped within a protein crystal

Structure:

LysozymE C. Chain: a. Fragment: lysozyme. Synonym: 1,4-beta-n-acetylmuramidasE C. Allergen gal d 4. Gal d iv. Ec: 3.2.1.17

Source:

Gallus gallus. Chicken. Organism_taxid: 9031

Resolution:

1.25Å R-factor: 0.182 R-free: 0.213

Ensemble:

10 models

Authors:

J.Ondracek,J.R.Mesters

Key ref:

J.Ondrácek and J.R.Mesters (2006). An ensemble of crystallographic models enables the description of novel bromate-oxoanion species trapped within a protein crystal. Acta Crystallogr D Biol Crystallogr, 62, 996-1001. PubMed id: 16929100 DOI: 10.1107/S0907444906021627

Date:

10-Nov-05 Release date: 29-Nov-05

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/S0907444906021627

Acta Crystallogr D Biol Crystallogr 62:996-1001 (2006)

PubMed id: 16929100

An ensemble of crystallographic models enables the description of novel bromate-oxoanion species trapped within a protein crystal.

J.Ondrácek, J.R.Mesters.

ABSTRACT

Only a few protein-oxoanion crystal complexes have been described to date. Here, the structure of a protein soaked in a bromate solution has been determined to a resolution of 1.25 A and refined to final overall R/R(free) values of 18.04/21.3 (isotropic) and 11.25/14.67 (anisotropic). In contrast to the single-model approach, refinement of an ensemble of ten models enabled us to determine variances and statistically evaluate bond-length distances and angles in the oxoanions. In total, nine bromate positions, including two BrO(3)(-) x HBrO(3) dimer species, have been identified on the basis of the anomalous signal of the Br atoms. For all bromate ions, the main-chain amide atoms of the protein were identified as the dominant binding positions, a useful property in any experimental phase-determination experiment.

Selected figure(s)

Figure 1.
Figure 1 Modelled and refined disorder of (a) Asp52 and (b) Pro79. The electron-density map is contoured at 1.7 (produced using PyMOL; DeLano, 2002[DeLano, W. L. (2002). The PyMOL Molecular Visualization System. DeLano Scientific, San Carlos, CA, USA.]).

Figure 2.
Figure 2 Examples of disorder generated by the refinement for (a) Arg21, (b) Arg61 and Arg73 and (c) Arg128 (produced using PyMOL; DeLano, 2002[DeLano, W. L. (2002). The PyMOL Molecular Visualization System. DeLano Scientific, San Carlos, CA, USA.]).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 996-1001) copyright 2006.

Figures were selected by an automated process.