8EY3 | pdb_00008ey3

Contact-dependent growth inhibition (CDI) immunity protein from E. coli O32:H37

• PDB DOI: https://doi.org/10.2210/pdb8EY3/pdb

• Classification: TOXIN
• Organism(s): Escherichia coli O32:H37
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-10-26 Released: 2023-11-08 
• Deposition Author(s): Michalska, K., Stols, L., Eschenfeldt, W., Goulding, C.W., Hayes, C.S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.110 (Depositor), 0.120 (DCC) 
• R-Value Work: 
  0.103 (Depositor), 0.113 (DCC) 
• R-Value Observed: 
  0.103 (Depositor) 

Literature

Contact-dependent growth inhibition (CDI) immunity protein from E. coli O32:H37

Michalska, K., Stols, L., Eschenfeldt, W., Goulding, C.W., Hayes, C.S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 7.08 kDa 
• Atom Count: 637 
• Modeled Residue Count: 60 
• Deposited Residue Count: 65 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cys_rich_CPCC domain-containing protein	A	65	Escherichia coli O32:H37	Mutation(s): 0  Gene Names:  B6R12_004683, B6R15_004523, C0P57_003609, D9E49_27105, DAH20_21150, DEN92_22940, DEN93_17480, DEO13_20945, DEO14_22190, DEO15_23150, E5S48_23695, E5S53_25065, E5S55_25155, FHQ91_23985, FJQ51_24360, FJQ53_24775, GF698_05830, GQW68_24765
UniProt
Find proteins for A0A1Y2XHL0 (Escherichia coli) Explore A0A1Y2XHL0  Go to UniProtKB:  A0A1Y2XHL0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE2 (Subject of Investigation/LOI)	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
NA	C [auth A], D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.110 (Depositor), 0.120 (DCC) 
• R-Value Work:  0.103 (Depositor), 0.113 (DCC) 
• R-Value Observed: 0.103 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.386	α = 90
b = 35.753	β = 90
c = 50.34	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-08 
Deposition Author(s): Michalska, K., Stols, L., Eschenfeldt, W., Goulding, C.W., Hayes, C.S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2023-11-08
  Type: Initial release
  
• Version 2.0: 2025-11-26
  Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary