9GQR | pdb_00009gqr

Structure of a consensus-designed decarboxylase (PSC1)

• PDB DOI: https://doi.org/10.2210/pdb9GQR/pdb

• Classification: LYASE
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-09-09 Released: 2025-05-21 
• Deposition Author(s): Gavira, J.A., Ramos, J.L., Garcia-Franco, A., de la Torre, J.
• Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN), European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.247 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: in silico

Literature

Sustainable synthesis of styrene exploiting a consensus-designed decarboxylase. Purification and crystal structure of PSC1

Garcia-Franco, A., de la Torre, J., Godoy, P., Duquez, E., Lopez, C., Gavira, J.A., Ramos, J.L.

(2025) mBio 

• DOI: https://doi.org/10.1128/mbio.00714.25

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 111.56 kDa 
• Atom Count: 8,330 
• Modeled Residue Count: 992 
• Deposited Residue Count: 1,004 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
decarboxylase	A, B	502	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], F [auth B], G [auth B], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	E [auth A], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.247 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.63	α = 71.67
b = 66.276	β = 73.08
c = 72.665	γ = 69.88

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Gavira, J.A., Ramos, J.L., Garcia-Franco, A., de la Torre, J.

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Funding Organization	Location	Grant Number
Ministerio de Ciencia e Innovacion (MCIN)	Spain	PID2021-123469OBI00
European Commission	European Union	EJPSOIL862695
Ministerio de Ciencia e Innovacion (MCIN)	Spain	PID2020-116261GB-I00

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release