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)

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
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Ligand Structure Quality Assessment

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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

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9EX54
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP (Subject of Investigation/LOI) Query on NDP Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
BTB (Subject of Investigation/LOI) Query on BTB Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-11-27

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.