1H5X | pdb_00001h5x

CRYSTAL STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-13 COMPLEXED WITH IMIPENEM

• PDB DOI: https://doi.org/10.2210/pdb1H5X/pdb

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


• Deposited: 2001-05-29 Released: 2002-05-23 
• Deposition Author(s): Mayer, C., Pernot, L., Sougakoff, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.246 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Acyl-Enzyme Intermediate Oxa-13:Imipenem

Pernot, L., Mayer, C., Sougakoff, W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 55.98 kDa 
• Atom Count: 4,129 
• Modeled Residue Count: 471 
• Deposited Residue Count: 494 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-LACTAMASE	A, B	247	Pseudomonas aeruginosa	Mutation(s): 0  EC: 3.5.2.6
UniProt
Find proteins for Q51400 (Pseudomonas aeruginosa) Explore Q51400  Go to UniProtKB:  Q51400

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IM2	C [auth A], G [auth B]	(5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid C12 H19 N3 O4 S UACUABDJLSUFFC-IWSPIJDZSA-N
SO4	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.246 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.22	α = 90
b = 82.06	β = 90
c = 125.14	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-23 
Deposition Author(s): Mayer, C., Pernot, L., Sougakoff, W.

Revision History  

• Version 1.0: 2002-05-23
  Type: Initial release
  
• Version 1.1: 2011-07-27
  Changes: Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
• Version 1.2: 2011-12-07
  Changes: Non-polymer description
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.4: 2025-10-01
  Changes: Advisory, Derived calculations, Structure summary