Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 55.25 kDa 
• Atom Count: 4500 
• Modelled Residue Count: 506 
• Deposited Residue Count: 512 
• Unique protein chains: 1

1DXE

2-dehydro-3-deoxy-galactarate aldolase from Escherichia coli

• PDB DOI: 10.2210/pdb1DXE/pdb

• Classification: CLASS II ALDOLASE
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2000-01-03 Released: 2000-08-25 
• Deposition Author(s): Izard, T., Blackwell, N.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.194 
• R-Value Work: 0.171 
• R-Value Observed: 0.171 

Literature

Crystal Structures of the Metal-Dependent 2-Dehydro-3-Deoxy-Galactarate Aldolase Suggest a Novel Reaction Mechanism.

Izard, T., Blackwell, N.C.

(2000) EMBO J 19: 3849

• PubMed: 10921867 
• DOI: 10.1093/emboj/19.15.3849
• Primary Citation of Related Structures:  
  1DXE, 1DXF


• PubMed Abstract: 
  

Carbon-carbon bond formation is an essential reaction in organic chemistry and the use of aldolase enzymes for the stereochemical control of such reactions is an attractive alternative to conventional chemical methods. Here we describe the crystal structures of a novel class II enzyme, 2-dehydro-3-deoxy-galactarate (DDG) aldolase from Escherichia coli, in the presence and absence of substrate. The crystal structure was determined by locating only four Se sites to obtain phases for 506 protein residues. The protomer displays a modified (alpha/beta)(8) barrel fold, in which the eighth alpha-helix points away from the beta-barrel instead of packing against it. Analysis of the DDG aldolase crystal structures suggests a novel aldolase mechanism in which a phosphate anion accepts the proton from the methyl group of pyruvate.

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Organizational Affiliation: 

Department of Biochemistry, University of Leicester, Leicester LE1 7RH, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE	A, B	256	Escherichia coli	Mutation(s): 0  EC: 4.1.2.20
UniProt
Find proteins for P23522 (Escherichia coli (strain K12)) Explore P23522  Go to UniProtKB:  P23522

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A], F [auth B], G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.194 
• R-Value Work: 0.171 
• R-Value Observed: 0.171 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.07	α = 90
b = 129.07	β = 90
c = 167.96	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-01-03 
• Released Date: 2000-08-25 
Deposition Author(s): Izard, T., Blackwell, N.C.

Revision History  

• Version 1.0: 2000-08-25
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance