4HD5 image
Deposition Date 2012-10-02
Release Date 2012-10-10
Last Version Date 2024-04-03
Entry Detail
PDB ID:
4HD5
Keywords:
Title:
Crystal Structure of BC0361, a polysaccharide deacetylase from Bacillus cereus
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.90 Å
R-Value Free:
0.20
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Polysaccharide deacetylase
Gene (Uniprot):BC_0361
Chain IDs:A
Chain Length:360
Number of Molecules:1
Biological Source:Bacillus cereus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
PXU A PRO 2-HYDROXY-L-PROLINE
Primary Citation
Structure determination through homology modelling and torsion-angle simulated annealing: application to a polysaccharide deacetylase from Bacillus cereus.
Acta Crystallogr.,Sect.D 69 276 283 (2013)
PMID: 23385463 DOI: 10.1107/S0907444912045829

Abstact

The structure of BC0361, a polysaccharide deacetylase from Bacillus cereus, has been determined using an unconventional molecular-replacement procedure. Tens of putative models of the C-terminal domain of the protein were constructed using a multitude of homology-modelling algorithms, and these were tested for the presence of signal in molecular-replacement calculations. Of these, only the model calculated by the SAM-T08 server gave a consistent and convincing solution, but the resulting model was too inaccurate to allow phase determination to proceed to completion. The application of slow-cooling torsion-angle simulated annealing (started from a very high temperature) drastically improved this initial model to the point of allowing phasing through cycles of model building and refinement to be initiated. The structure of the protein is presented with emphasis on the presence of a C(α)-modified proline at its active site, which was modelled as an α-hydroxy-L-proline.

Legend

Protein

Chemical

Disease

Primary Citation of related structures