6ZRP

Crystal structure of class D Beta-lactamase OXA-48 in complex with meropenem

• PDB DOI: https://doi.org/10.2210/pdb6ZRP/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-14 Released: 2021-07-21 
• Deposition Author(s): Tassone, G., De Luca, F., Pozzi, C., Di Pisa, F., Benvenuti, M., Mangani, S., Doquier, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.187 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 

Starting Model: experimental

Literature

Mechanistic insights into carbapenem hydrolysis by OXA-48 and the OXA10-derived hybrids OXA-10 loop24 and loop48

Tassone, G., De Luca, F., Pozzi, C., Di Pisa, F., Benvenuti, M., Mangani, S., Doquier, J.D.

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.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 124.43 kDa 
• Atom Count: 9,498 
• Modelled Residue Count: 970 
• Deposited Residue Count: 1,060 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, D	265	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: bla OXA-48, blaOXA-48, KPE71T_00045 EC: 3.5.2.6
UniProt
Find proteins for Q6XEC0 (Klebsiella pneumoniae) Explore Q6XEC0  Go to UniProtKB:  Q6XEC0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	B, C	265	Klebsiella pneumoniae	Mutation(s): 0  Gene Names:  bla OXA-48, bla_1, bla_2, bla_5, blaOXA-48, B6R99_29845, GJD56_28020, GJJ04_29145, KPE71T_00045, SAMEA3538918_02768, SAMEA3538961_03054, SAMEA3673128_05462 EC: 3.5.2.6
UniProt
Find proteins for Q6XEC0 (Klebsiella pneumoniae) Explore Q6XEC0  Go to UniProtKB:  Q6XEC0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DWZ (Subject of Investigation/LOI)	E [auth A], J [auth B], P [auth C], V [auth D]	(2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid C17 H27 N3 O5 S UUIYVKJXUXGPKB-VGWSNGFZSA-N
EDO	AA [auth D], BA [auth D], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth C], W [auth D], X [auth D], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, D	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.187 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.994	α = 90
b = 125.286	β = 77.7
c = 105.199	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-21 
Deposition Author(s): Tassone, G., De Luca, F., Pozzi, C., Di Pisa, F., Benvenuti, M., Mangani, S., Doquier, J.D.

Revision History  

• Version 1.0: 2021-07-21
  Type: Initial release
  
• Version 1.1: 2022-02-02
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description