7PEH

Crystal Structure of a Class D Carbapenemase

• PDB DOI: https://doi.org/10.2210/pdb7PEH/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-08-10 Released: 2022-08-24 
• Deposition Author(s): Zhou, Q., He, Y., Jin, Y.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.249 
• R-Value Work: 0.218 

Starting Model: experimental

Literature

An Ion-Pair Induced Intermediate Complex Captured in Class D Carbapenemase Reveals Chloride Ion as a Janus Effector Modulating Activity

Zhou, Q., Catalan, P., Bell, H., Baumann, P., Cooke, R., Evans, R., Yang, J., Zhang, Z., Zappala, D., Zhang, Y., Blackburn, G.M., He, Y., Jin, Y.

(2023) ACS Cent Sci 

• DOI: https://doi.org/10.1021/acscentsci.3c00609

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: 121.54 kDa 
• Atom Count: 8,445 
• Modelled Residue Count: 968 
• Deposited Residue Count: 1,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	260	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: bla OXA-48, bla_2, blaOXA-48, G5637_27540, KPE71T_00045, SAMEA3649466_05396 EC: 3.5.2.6
UniProt
Find proteins for Q6XEC0 (Klebsiella pneumoniae) Explore Q6XEC0  Go to UniProtKB:  Q6XEC0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1BO	E [auth AAA], F [auth AAA], G [auth AAA], H [auth BBB], I [auth BBB], J [auth CCC], K [auth DDD]	1-BUTANOL C4 H10 O LRHPLDYGYMQRHN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.249 
• R-Value Work: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.003	α = 90
b = 106.976	β = 90
c = 124.611	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Zhou, Q., He, Y., Jin, Y.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	31400663

Revision History  

• Version 1.0: 2022-08-24
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-03-06
  Changes: Database references