5E2E

Crystal Structure of Beta-lactamase Precursor BlaA from Yersinia enterocolitica

• PDB DOI: https://doi.org/10.2210/pdb5E2E/pdb

• Classification: HYDROLASE
• Organism(s): Yersinia enterocolitica subsp. enterocolitica 8081
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-10-01 Released: 2015-10-28 
• Deposition Author(s): Kim, Y., Joachimiak, G., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.243 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Literature

Crystal Structure of Beta-lactamase Precursor BlaA from Yersinia enterocolitica

Kim, Y., Joachimiak, G., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 58.29 kDa 
• Atom Count: 4,190 
• Modelled Residue Count: 520 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	269	Yersinia enterocolitica subsp. enterocolitica 8081	Mutation(s): 0  Gene Names: blaA, YE2019 EC: 3.5.2.6
UniProt
Find proteins for A1JML9 (Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)) Explore A1JML9  Go to UniProtKB:  A1JML9

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.243 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.116	α = 90
b = 93.513	β = 90
c = 122.219	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-10-28 
Deposition Author(s): Kim, Y., Joachimiak, G., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2015-10-28
  Type: Initial release
  
• Version 1.1: 2022-04-13
  Changes: Author supporting evidence, Data collection, Database references, Derived calculations
• Version 1.2: 2024-10-16
  Changes: Data collection, Structure summary