7EMG | pdb_00007emg

Carbonyl Reductase Variant 4 (R123C/L209P/F183Y/V61K) from Serratia marcescens complexed with NADP+

• PDB DOI: https://doi.org/10.2210/pdb7EMG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Serratia marcescens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-04-14 Released: 2021-10-06 
• Deposition Author(s): Zheng, Y.C., Wang, T., Bai, Y.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.259 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Stereoselective synthesis of chiral delta-lactones via an engineered carbonyl reductase.

Wang, T., Zhang, X.Y., Zheng, Y.C., Bai, Y.P.

(2021) Chem Commun (Camb) 57: 10584-10587

• PubMed: 34559867 
• DOI: https://doi.org/10.1039/d1cc04542c
• Primary Citation Related Structures: 
  7EMG


• PubMed Abstract: 
  

  A carbonyl reductase variant, Sm CR _M5 , from Serratia marcescens was obtained through structure-guided directed evolution. The variant showed improved specific activity (U mg ^-1 ) towards most of the 16 tested substrates and gave high stereoselectivities of up to 99% in the asymmetric synthesis of 13 γ-/δ-lactones. In particular, SmCR _M5 showed a 13.8-fold higher specific activity towards the model substrate, i.e. , 5-oxodecanoic acid, and gave ( R )-δ-decalactone in 99% ee with a space-time yield (STY) of 301 g L ^-1 d ^-1 . The preparative synthesis of six δ-lactones in high yields and with high enantiopurities showed the feasibility of the biocatalytic synthesis of these high-value-added chemicals, providing a cost-effective and green alternative to noble-metal catalysis.

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Organizational Affiliation: 
• State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 54.8 kDa 
• Atom Count: 3,621 
• Modeled Residue Count: 476 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] reductase	A, B	252	Serratia marcescens	Mutation(s): 4  Gene Names: fabG, A8A12_06940, AR325_11665, BVG93_06205, G3M86_05635, G3M87_05635, G3M88_05635, G3M89_05635, GV243_09700, HMI62_09690 EC: 1.1.1.100

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], E [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.259 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.841	α = 90
b = 120.299	β = 90
c = 120.664	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-10-06 
Deposition Author(s): Zheng, Y.C., Wang, T., Bai, Y.P.

Revision History  

• Version 1.0: 2021-10-06
  Type: Initial release
  
• Version 1.1: 2022-02-16
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description