8SSM | pdb_00008ssm

Citrobacter rodentium contact dependent growth inhibition (CDI) toxin (CdiA-CT) and immunity (CdiI) complex

PDB DOI: https://doi.org/10.2210/pdb8SSM/pdb

Classification: TOXIN
Organism(s): Citrobacter rodentium
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-05-08 Released: 2024-05-15
Deposition Author(s): Cuthbert, B.J., Goulding, C.W., Hayes, C.S., Nhan, D.Q.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free:
0.237 (Depositor), 0.237 (DCC)
R-Value Work:
0.187 (Depositor), 0.196 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Models: in silico, experimental
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This is version 1.0 of the entry. See complete history.

Literature

Structural and biochemical studies into Citrobacter rodentium contact dependent growth inhibition (CDI) peptidase toxin

Cuthbert, B.J., Goulding, C.W., Hayes, C.S., Nhan, D.Q.

To be published.

Macromolecule Content

Total Structure Weight: 53.57 kDa
Atom Count: 3,850
Modeled Residue Count: 465
Deposited Residue Count: 476
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Contact-dependent inhibitor A	A [auth B], C [auth A]	143	Citrobacter rodentium	Mutation(s): 1 Gene Names: stbD, E2R62_11320
UniProt
Find proteins for A0A482PFX0 (Citrobacter rodentium) Explore A0A482PFX0 Go to UniProtKB: A0A482PFX0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A482PFX0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CdiI (immunity protein)	B [auth C], D	95	Citrobacter rodentium	Mutation(s): 0 Gene Names: ROD_29401
UniProt
Find proteins for D2TJN9 (Citrobacter rodentium (strain ICC168)) Explore D2TJN9 Go to UniProtKB: D2TJN9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D2TJN9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain F [auth A] MOL2 format, chain E [auth C] MOL2 format, chain F [auth A] mmCIF format, chain E [auth C] mmCIF format, chain F [auth A]	E [auth C], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Focus chain F [auth A] Interactions & Density Focus chain E [auth C] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.237 (Depositor), 0.237 (DCC)
R-Value Work: 0.187 (Depositor), 0.196 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.349	α = 90
b = 114.41	β = 90
c = 114.639	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-15

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2024-05-15
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.