8EY4 | pdb_00008ey4

Contact-dependent growth inhibition toxin-immunity protein complex from E. coli O32:H37

PDB DOI: https://doi.org/10.2210/pdb8EY4/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.202 (Depositor), 0.207 (DCC)
R-Value Work:
0.157 (Depositor), 0.160 (DCC)
R-Value Observed:
0.161 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Contact-dependent growth inhibition toxin-immunity protein complex 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.

Macromolecule Content

Total Structure Weight: 17.87 kDa
Atom Count: 1,238
Modeled Residue Count: 146
Deposited Residue Count: 158
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cys_rich_CPCC domain-containing protein	A [auth I]	70	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... 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1Y2XHL0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PT-VENN domain-containing protein	B [auth A]	88	Escherichia coli O32:H37	Mutation(s): 0 Gene Names: LH0189
UniProt
Find proteins for Q3ZTX4 (Escherichia coli) Explore Q3ZTX4 Go to UniProtKB: Q3ZTX4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3ZTX4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE2 (Subject of Investigation/LOI) Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain C [auth I] MOL2 format, chain C [auth I] mmCIF format, chain C [auth I]	C [auth I]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain C [auth I] Interactions & Density Focus chain C [auth I]

Modified Residues 1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE Query on MSE	B [auth A]	MET	Selenomethionine	C₅ H₁₁ N O₂ Se

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.202 (Depositor), 0.207 (DCC)
R-Value Work: 0.157 (Depositor), 0.160 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.641	α = 90
b = 53.66	β = 102.55
c = 38.533	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-11-08

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Center for Structural Genomics of Infectious Diseases (CSGID)

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

Revision History (Full details and data files)

Version 1.0: 2023-11-08
Type: Initial release
Version 1.1: 2023-11-15
Changes: Data collection
Version 1.2: 2024-10-23
Changes: Structure summary
Version 2.0: 2025-11-26
Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary