8AVZ | pdb_00008avz

Crystal structure of PksD, the trans-acting acyl hydrolase domain from the bacillaene trans-AT PKS (SeMet derivative)

• PDB DOI: https://doi.org/10.2210/pdb8AVZ/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-08-28 Released: 2023-08-09 
• Deposition Author(s): Fage, C.D., Challis, G.L., Lewandowski, J., Jenner, M.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Molecular Basis for Short-Chain Thioester Hydrolysis by Acyl Hydrolases in trans-Acyltransferase Polyketide Synthases

Fage, C.D., Passmore, M., Tatman, B.P., Smith, H.G., Jian, X., Dissanayake, U.C., Foran, M.E., Cisneros, G.A., Challis, G.L., Lewandowski, J.R., Jenner, M.

(2025) JACS Au 

• DOI: https://doi.org/10.1021/jacsau.4c00837

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 150.93 kDa 
• Atom Count: 10,968 
• Modeled Residue Count: 1,262 
• Deposited Residue Count: 1,308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyketide biosynthesis acyltransferase homolog PksD	A, B, C, D	327	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: pksD, BSU17110 EC: 2.3.1
UniProt
Find proteins for O34877 (Bacillus subtilis (strain 168)) Explore O34877  Go to UniProtKB:  O34877

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 207.708	α = 90
b = 83.564	β = 119.71
c = 145.742	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
PHENIX	refinement
PHENIX	phasing
Aimless	data scaling
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-09 
Deposition Author(s): Fage, C.D., Challis, G.L., Lewandowski, J., Jenner, M.

---

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	--

Revision History  

• Version 1.0: 2023-08-09
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Structure summary
• Version 1.2: 2025-02-05
  Changes: Database references