8SSK | pdb_00008ssk

Citrobacter rodentium contact dependent growth inhibition (CDI) entry and toxin (CdiA-CT) domains

PDB DOI: https://doi.org/10.2210/pdb8SSK/pdb

Classification: TOXIN
Organism(s): Citrobacter rodentium
Expression System: Escherichia coli
Mutation(s): No

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: 1.90 Å
R-Value Free:
0.194 (Depositor), 0.194 (DCC)
R-Value Work:
0.166 (Depositor), 0.166 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Models: experimental, in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 3.0 of the entry. See complete history.

Literature

Citrobacter rodentium contact dependent growth inhibition (CDI) entry and toxin (CdiA-CT) domains

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

To be published.

Macromolecule Content

Total Structure Weight: 136.69 kDa
Atom Count: 10,307
Modeled Residue Count: 1,219
Deposited Residue Count: 1,272
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fimbrial usher protein StbD	A, B, C, D	318	Citrobacter rodentium	Mutation(s): 0 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain J [auth A] SDF format, chain E [auth A] SDF format, chain BA [auth C] MOL2 format, chain R [auth C] MOL2 format, chain J [auth A] MOL2 format, chain E [auth A] MOL2 format, chain BA [auth C] mmCIF format, chain R [auth C] mmCIF format, chain J [auth A] mmCIF format, chain E [auth A] mmCIF format, chain BA [auth C]	BA [auth C], E [auth A], J [auth A], R [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth C] Focus chain E [auth A] Focus chain J [auth A] Focus chain R [auth C] Interactions & Density Focus chain BA [auth C] Focus chain E [auth A] Focus chain J [auth A] Focus chain R [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain IA [auth D] SDF format, chain HA [auth D] SDF format, chain H [auth A] SDF format, chain GA [auth D] SDF format, chain FA [auth D] SDF format, chain F [auth A] SDF format, chain AA [auth C] MOL2 format, chain S [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain IA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain AA [auth C] mmCIF format, chain S [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain IA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain AA [auth C]	AA [auth C] F [auth A] FA [auth D] GA [auth D] H [auth A] AA [auth C], F [auth A], FA [auth D], GA [auth D], H [auth A], HA [auth D], IA [auth D], N [auth B], O [auth B], P [auth B], S [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain F [auth A] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Interactions & Density Focus chain AA [auth C] Focus chain F [auth A] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain JA [auth D] SDF format, chain I [auth A] SDF format, chain G [auth A] SDF format, chain EA [auth D] SDF format, chain DA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain JA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain DA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain JA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain DA [auth D]	DA [auth D] EA [auth D] G [auth A] I [auth A] JA [auth D] DA [auth D], EA [auth D], G [auth A], I [auth A], JA [auth D], L [auth B], M [auth B], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain I [auth A] Focus chain JA [auth D] Focus chain L [auth B] Focus chain M [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain I [auth A] Focus chain JA [auth D] Focus chain L [auth B] Focus chain M [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain KA [auth D] SDF format, chain K [auth A] SDF format, chain CA [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain KA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain CA [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain KA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain CA [auth C]	CA [auth C], K [auth A], KA [auth D], Q [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain K [auth A] Focus chain KA [auth D] Focus chain Q [auth B] Interactions & Density Focus chain CA [auth C] Focus chain K [auth A] Focus chain KA [auth D] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.194 (Depositor), 0.194 (DCC)
R-Value Work: 0.166 (Depositor), 0.166 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.87	α = 90
b = 113.982	β = 92.388
c = 87.351	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

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
Version 1.1: 2024-10-09
Changes: Structure summary
Version 2.0: 2025-03-05
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 3.0: 2025-04-02
Type: Coordinate replacement
Reason: Model orientation/position
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary