3I1C | pdb_00003i1c

Crystal Structure of a Novel Engineered Diels-Alderase: DA_20_00_A74I

• PDB DOI: https://doi.org/10.2210/pdb3I1C/pdb

• Classification: HYDROLASE
• Organism(s): Loligo vulgaris
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-06-26 Released: 2009-08-18 
• Deposition Author(s): Lambert, A.R., Stoddard, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.253 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.

Siegel, J.B., Zanghellini, A., Lovick, H.M., Kiss, G., Lambert, A.R., St Clair, J.L., Gallaher, J.L., Hilvert, D., Gelb, M.H., Stoddard, B.L., Houk, K.N., Michael, F.E., Baker, D.

(2010) Science 329: 309-313

• PubMed: 20647463 
• DOI: https://doi.org/10.1126/science.1190239
• Primary Citation Related Structures: 
  3I1C


• PubMed Abstract: 
  

  The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity. X-ray crystallography confirms that the structure matches the design for the most active of the enzymes, and binding site substitutions reprogram the substrate specificity. Designed stereoselective catalysts for carbon-carbon bond-forming reactions should be broadly useful in synthetic chemistry.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.19 kDa 
• Atom Count: 2,787 
• Modeled Residue Count: 314 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diisopropyl-fluorophosphatase	A	324	Loligo vulgaris	Mutation(s): 14  EC: 3.1.8.2 (PDB Primary Data), 3.8.2.2 (UniProt)
UniProt
Find proteins for Q7SIG4 (Loligo vulgaris) Explore Q7SIG4  Go to UniProtKB:  Q7SIG4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.253 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.239	α = 90
b = 83.112	β = 90
c = 85.18	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-18 
Deposition Author(s): Lambert, A.R., Stoddard, B.L.

Revision History  

• Version 1.0: 2009-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.3: 2024-02-21
  Changes: Data collection