3C5A

Crystal structure of the C-terminal deleted mutant of the class A carbapenemase KPC-2 at 1.23 angstrom

• PDB DOI: https://doi.org/10.2210/pdb3C5A/pdb

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


• Deposited: 2008-01-31 Released: 2008-08-05 
• Deposition Author(s): Petrella, S., Ziental-Gelus, N., Mayer, C., Jarlier, V., Sougakoff, W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free: 0.196 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 

Starting Model: experimental

Literature

Genetic and structural insights into the dissemination potential of the extremely-broad-spectrum class A {beta}-lactamase (EBSBL) KPC-2 identified in two strains of Escherichia coli and Enterobacter cloacae isolated from the same patient in France

Petrella, S., Ziental-Gelus, N., Mayer, C., Renard, M., Jarlier, V., Sougakoff, W.

(2008) Antimicrob Agents Chemother 

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: 28.18 kDa 
• Atom Count: 2,168 
• Modelled Residue Count: 264 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Class A carbapenemase KPC-2	A	264	Escherichia coli	Mutation(s): 0  EC: 3.5.2.6
UniProt
Find proteins for A8DS27 (Escherichia coli) Explore A8DS27  Go to UniProtKB:  A8DS27

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	B [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free: 0.196 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.89	α = 90
b = 65.99	β = 90
c = 72.13	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Xnemo	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-05 
Deposition Author(s): Petrella, S., Ziental-Gelus, N., Mayer, C., Jarlier, V., Sougakoff, W.

Revision History  

• Version 1.0: 2008-08-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary