8V1X | pdb_00008v1x

Crystal structure of polyketide synthase (PKS) thioreductase domain from Streptomyces coelicolor

• PDB DOI: https://doi.org/10.2210/pdb8V1X/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptomyces coelicolor
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-11-21 Released: 2024-11-27 
• Deposition Author(s): Pereira, J.H., Dan, Q., Keasling, J., Adams, P.D.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: in silico

Literature

A polyketide-based biosynthetic platform for diols, amino alcohols and hydroxy acids

Dan, Q., Chiu, Y., Lee, N., Pereira, J.H., Rad, B., Zhao, X., Deng, K., Rong, Y., Zhan, C., Chen, Y., Cheong, S., Li, C., Gin, J.W., Rodrigues, A., Northen, T.R., Backman, T.W.H., Baidoo, E.E.K., Petzold, C.J., Adams, P.D., Keasling, J.D.

(2025) Nat Catal 8: 147-161

• DOI: https://doi.org/10.1038/s41929-025-01299-5

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 89.59 kDa 
• Atom Count: 6,566 
• Modeled Residue Count: 776 
• Deposited Residue Count: 802 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type I polyketide synthase	A, B	401	Streptomyces coelicolor	Mutation(s): 0  Gene Names: SCO6273
UniProt
Find proteins for Q9EX54 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9EX54  Go to UniProtKB:  Q9EX54

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP (Subject of Investigation/LOI)	C [auth A], F [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
BTB (Subject of Investigation/LOI)	E [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)	D [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.635	α = 90
b = 103.546	β = 90
c = 148.316	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-27 
Deposition Author(s): Pereira, J.H., Dan, Q., Keasling, J., Adams, P.D.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-AC02-05CH11231

Revision History  

• Version 1.0: 2024-11-27
  Type: Initial release
  
• Version 1.1: 2025-06-11
  Changes: Database references