4QD8 | pdb_00004qd8

Crystal structure of Thioesterase PA1618 from Pseudomonas aeruginosa in complex with phenacyl-CoA

• PDB DOI: https://doi.org/10.2210/pdb4QD8/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-05-13 Released: 2015-05-13 
• Deposition Author(s): Ji, T., Allen, K.N., Dunaway-Mariano, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Design and Use of an Ester Analog of CoA to Trap the Michaelis Complex in a Thioesterase

Latham, J.A., Ji, T., Matthews, K., Allen, K.N., Dunaway-Mariano, D.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 103.3 kDa 
• Atom Count: 7,082 
• Modeled Residue Count: 834 
• Deposited Residue Count: 912 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioesterase PA1618	A, B, C, D, E, F	152	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: PA1618 EC: 3.1.2
UniProt
Find proteins for Q9I3A4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I3A4  Go to UniProtKB:  Q9I3A4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0FQ	G [auth C], H [auth C], I [auth D], J [auth D]	phenacyl coenzyme A C29 H42 N7 O17 P3 S WOEFYXMDPBOUAP-VXAHOBLNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.687	α = 90
b = 202.005	β = 90
c = 91.083	γ = 90

Software Package:

Software Name	Purpose
JBluIce-EPICS	data collection
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-13 
Deposition Author(s): Ji, T., Allen, K.N., Dunaway-Mariano, D.

Revision History  

• Version 1.0: 2015-05-13
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations