8KBD

Structure of CmTad1 complexed with cAAG

• PDB DOI: https://doi.org/10.2210/pdb8KBD/pdb
• NAKB: 8KBD

• Classification: VIRAL PROTEIN/RNA
• Organism(s): Clostridioides mangenotii LM2, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-08-04 Released: 2024-08-07 
• Deposition Author(s): Xiao, Y., Feng, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.239 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 

Starting Model: in silico

Literature

Structure of CmTad1 complexed with cAAG

Xiao, Y., Feng, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 186.3 kDa 
• Atom Count: 12,885 
• Modelled Residue Count: 1,574 
• Deposited Residue Count: 1,596 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thoeris anti-defense 1	A, B, C [auth G], D [auth H], E [auth I], F [auth J], G [auth K], H [auth L], I [auth C], J [auth D], K [auth E], L [auth F]	132	Clostridioides mangenotii LM2	Mutation(s): 0  Gene Names: tad1
UniProt
Find proteins for P0DW61 (Clostridioides mangenotii (strain LM2)) Explore P0DW61  Go to UniProtKB:  P0DW61

Entity ID: 2
Molecule	Chains	Length	Organism	Image
cAAG	M [auth N], N [auth O], O [auth P], P [auth Q]	3	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	Q [auth A], R [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.239 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.719	α = 90
b = 145.072	β = 90
c = 149.989	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
xia2	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Xiao, Y., Feng, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release