9ILD | pdb_00009ild

Complex structure of Cap3 and CD-NTase

• PDB DOI: https://doi.org/10.2210/pdb9ILD/pdb

• Classification: ANTIFUNGAL PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-29 Released: 2024-07-31 
• Deposition Author(s): Li, F.Q., Ma, W.F.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.283 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: in silico

Literature

Structural and functional characterization of the bacterial Cap3 enzyme in deconjugation and regulation of the cyclic dinucleotide transferase CD-NTase

Li, F.Q., Ma, W.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.09 kDa 
• Atom Count: 1,481 
• Modeled Residue Count: 178 
• Deposited Residue Count: 183 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase	A	156	Escherichia coli	Mutation(s): 0  Gene Names: GOP25_26465 EC: 3.4
UniProt
Find proteins for P0DTF3 (Escherichia coli (strain TW11681)) Explore P0DTF3  Go to UniProtKB:  P0DTF3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic GMP-AMP synthase	B	27	Escherichia coli	Mutation(s): 0  Gene Names: ETECE562_01214 EC: 2.7.7
UniProt
Find proteins for P0DTF0 (Escherichia coli (strain TW11681)) Explore P0DTF0  Go to UniProtKB:  P0DTF0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.283 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.051	α = 90
b = 54.843	β = 90
c = 59.606	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-31 
Deposition Author(s): Li, F.Q., Ma, W.F.

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Funding Organization	Location	Grant Number
Other government		--

Revision History  

• Version 1.0: 2024-07-31
  Type: Initial release