4F94 | pdb_00004f94

Structure of the Class D Beta-Lactamase OXA-24 K84D in Acyl-Enzyme Complex with Oxacillin

• PDB DOI: https://doi.org/10.2210/pdb4F94/pdb

• Classification: Hydrolase/Antibiotic
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-05-18 Released: 2013-08-14 
• Deposition Author(s): June, C.M., Vallier, B.C., Bonomo, R.A., Leonard, D.A., Powers, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.214 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Structure of the Class D Beta-Lactamase OXA-24 K84D in Acyl-Enzyme Complex with Oxacillin

June, C.M., Vallier, B.C., Bonomo, R.A., Leonard, D.A., Powers, R.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 28.45 kDa 
• Atom Count: 2,138 
• Modeled Residue Count: 245 
• Deposited Residue Count: 245 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	245	Acinetobacter baumannii	Mutation(s): 1  Gene Names: bla, bla-OXA-40, blaOXA-24, blaOXA-33, blaOXA-40, oxa-24, oxa40 EC: 3.5.2.6
UniProt
Find proteins for Q8RLA6 (Acinetobacter baumannii) Explore Q8RLA6  Go to UniProtKB:  Q8RLA6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1S6	B [auth A]	(2R,4S)-5,5-dimethyl-2-[(1R)-1-{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}-2-oxoethyl]-1,3-thiazolidine-4-carb oxylic acid C19 H21 N3 O5 S QXXMSXCGXIRLPM-ISTRZQFTSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.214 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.334	α = 90
b = 102.334	β = 90
c = 87.444	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-14 
Deposition Author(s): June, C.M., Vallier, B.C., Bonomo, R.A., Leonard, D.A., Powers, R.A.

Revision History  

• Version 1.0: 2013-08-14
  Type: Initial release
  
• Version 1.1: 2013-10-09
  Changes: Non-polymer description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary