8AVZ

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
R-Value Work: 0.179
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural basis for acyl hydrolysis in trans-AT polyketide synthases

Fage, C.D., Passmore, M., Tatman, B., Smith, H.G., Jian, X., Mudiyanselage, U.C.M., Berger, M., Cisneros, A.G., Challis, G.L., Lewandowski, J.R., Jenner, M.

To be published.

Macromolecule Content

Total Structure Weight: 150.93 kDa
Atom Count: 10,968
Modelled Residue Count: 1,262
Deposited Residue Count: 1,308
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	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 E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B]	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.179
R-Value Observed: 0.180
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

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.