4QD9 | pdb_00004qd9

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

PDB DOI: https://doi.org/10.2210/pdb4QD9/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.224 (Depositor), 0.220 (DCC)
R-Value Work:
0.186 (Depositor), 0.190 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 101.31 kDa
Atom Count: 7,108
Modeled Residue Count: 834
Deposited Residue Count: 912
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioesterase PA1618	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9I3A4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
31B Query on 31B Download Ideal Coordinates CCD File SDF format, chain H [auth F] SDF format, chain G [auth D] MOL2 format, chain H [auth F] MOL2 format, chain G [auth D] mmCIF format, chain H [auth F] mmCIF format, chain G [auth D]	G [auth D], H [auth F]	benzoyl-oxydephosphocoenzyme A C₂₈ H₃₉ N₇ O₁₅ P₂ KLLSEACSJWFZEP-NKRQLCBBSA-N		Interactions Focus chain G [auth D] Focus chain H [auth F] Interactions & Density Focus chain G [auth D] Focus chain H [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.224 (Depositor), 0.220 (DCC)
R-Value Work: 0.186 (Depositor), 0.190 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.026	α = 90
b = 201.49	β = 90
c = 91.744	γ = 90

Software Package:

Software Name	Purpose
autoXDS	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-05-13

Deposition Author(s):

Dunaway-Mariano, D.

Revision History (Full details and data files)

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

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.