6ZRI

Crystal structure of OXA-10loop24 in complex with meropenem

• PDB DOI: https://doi.org/10.2210/pdb6ZRI/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): No 


• Deposited: 2020-07-13 Released: 2021-07-21 
• Deposition Author(s): Tassone, G., Di Pisa, F., Benvenuti, M., De Luca, F., Pozzi, C., Mangani, S., Docquier, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.207 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

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

Tassone, G., Di Pisa, F., Benvenuti, M., De Luca, F., Pozzi, C., Mangani, S., Docquier, 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 and generated by PISA (software)

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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 111.8 kDa 
• Atom Count: 9,159 
• Modelled Residue Count: 970 
• Deposited Residue Count: 972 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C, D	243	Escherichia coli	Mutation(s): 0  Gene Names: blaoxa-10, blaOXA-10, oxa-10, BK373_28375, CQP61_30695, E4K55_27185, FORC82_p097, GII67_09965 EC: 3.5.2.6
UniProt
Find proteins for Q7BNC2 (Escherichia coli) Explore Q7BNC2  Go to UniProtKB:  Q7BNC2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DWZ (Subject of Investigation/LOI)	G [auth A], K [auth B], P [auth C], S [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	E [auth A], F [auth A], H [auth A], I [auth A], J [auth B], L [auth B], M [auth B], N [auth B], O [auth C], Q [auth D], R [auth D], T [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.207 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.64	α = 90
b = 80.64	β = 90
c = 152.29	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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