8AW0 | pdb_00008aw0

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

PDB DOI: https://doi.org/10.2210/pdb8AW0/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: 2.20 Å
R-Value Free:
0.227 (Depositor), 0.228 (DCC)
R-Value Work:
0.198 (Depositor), 0.199 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 297.35 kDa
Atom Count: 20,885
Modeled Residue Count: 2,534
Deposited Residue Count: 2,616
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyketide biosynthesis acyltransferase homolog PksD	A, B, C, D, E A, B, C, D, E, F, G, H	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O34877
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth E] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth E]	I [auth A], J [auth B], K [auth C], L [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth E] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.227 (Depositor), 0.228 (DCC)
R-Value Work: 0.198 (Depositor), 0.199 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.202	α = 90
b = 163.33	β = 104.5
c = 186.871	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-08-09

Deposition Author(s):

Lewandowski, J.

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

Revision History (Full details and data files)

Version 1.0: 2023-08-09
Type: Initial release
Version 1.1: 2024-06-19
Changes: Data collection
Version 1.2: 2024-11-27
Changes: Database references, Structure summary
Version 1.3: 2025-02-05
Changes: Database references

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.