4B9A | pdb_00004b9a

Structure of a putative epoxide hydrolase from Pseudomonas aeruginosa.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.138 (Depositor), 0.154 (DCC) 
  • R-Value Work: 
    0.111 (Depositor), 0.131 (DCC) 
  • R-Value Observed: 
    0.112 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4B9A

This is version 1.2 of the entry. See complete history

Literature

The Aeropath Project Targeting Pseudomonas Aeruginosa: Crystallographic Studies for Assessment of Potential Targets in Early-Stage Drug Discovery.

Moynie, L.Schnell, R.Mcmahon, S.A.Sandalova, T.Boulkerou, W.A.Schmidberger, J.W.Alphey, M.Cukier, C.Duthie, F.Kopec, J.Liu, H.Jacewicz, A.Hunter, W.N.Naismith, J.H.Schneider, G.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 25

  • DOI: https://doi.org/10.1107/S1744309112044739
  • Primary Citation Related Structures: 
    2XU8, 4AVF, 4AVR, 4AVY, 4B79, 4B7C, 4B7X, 4B9A, 4B9E, 4ES6, 4ETR, 4EXA, 4EXB

  • PubMed Abstract: 

    Bacterial infections are increasingly difficult to treat owing to the spread of antibiotic resistance. A major concern is Gram-negative bacteria, for which the discovery of new antimicrobial drugs has been particularly scarce. In an effort to accelerate early steps in drug discovery, the EU-funded AEROPATH project aims to identify novel targets in the opportunistic pathogen Pseudomonas aeruginosa by applying a multidisciplinary approach encompassing target validation, structural characterization, assay development and hit identification from small-molecule libraries. Here, the strategies used for target selection are described and progress in protein production and structure analysis is reported. Of the 102 selected targets, 84 could be produced in soluble form and the de novo structures of 39 proteins have been determined. The crystal structures of eight of these targets, ranging from hypothetical unknown proteins to metabolic enzymes from different functional classes (PA1645, PA1648, PA2169, PA3770, PA4098, PA4485, PA4992 and PA5259), are reported here. The structural information is expected to provide a firm basis for the improvement of hit compounds identified from fragment-based and high-throughput screening campaigns.


  • Organizational Affiliation
    • Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, Scotland.

Macromolecule Content 

  • Total Structure Weight: 35.14 kDa 
  • Atom Count: 2,961 
  • Modeled Residue Count: 298 
  • Deposited Residue Count: 301 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROBABLE EPOXIDE HYDROLASE301Pseudomonas aeruginosa PAO1Mutation(s): 0 
UniProt
Find proteins for Q9I229 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I229 
Go to UniProtKB:  Q9I229
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I229
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.138 (Depositor), 0.154 (DCC) 
  • R-Value Work:  0.111 (Depositor), 0.131 (DCC) 
  • R-Value Observed: 0.112 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.91α = 90
b = 83.91β = 90
c = 140.73γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-06
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.2: 2025-10-01
    Changes: Advisory, Derived calculations, Structure summary