8S47 | pdb_00008s47

CdaA-D07 complex

• PDB DOI: https://doi.org/10.2210/pdb8S47/pdb

• Classification: PROTEIN BINDING
• Organism(s): Listeria monocytogenes
• Expression System: Escherichia phage EcSzw-2
• Mutation(s): No 


• Deposited: 2024-02-21 Released: 2024-06-19 
• Deposition Author(s): Neumann, P., Ficner, R.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.240 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.206 (Depositor) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

CdaA-D07 complex

Neumann, P., Ficner, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.3 kDa 
• Atom Count: 2,495 
• Modeled Residue Count: 308 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diadenylate cyclase	A, B	178	Listeria monocytogenes	Mutation(s): 0  Gene Names: dacA, cdaA, lmo2120 EC: 2.7.7.85
UniProt
Find proteins for Q8Y5E4 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y5E4  Go to UniProtKB:  Q8Y5E4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
47U (Subject of Investigation/LOI)	C [auth A], E [auth B]	N-(pyridin-2-yl)-2-(1,3,5-trimethyl-1H-pyrazol-4-yl)acetamide C13 H16 N4 O OGOQOFZVILXVSY-UHFFFAOYSA-N
CL	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.240 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.206 (Depositor) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.22	α = 90
b = 65.07	β = 90
c = 130.33	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-06-19 
Deposition Author(s): Neumann, P., Ficner, R.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SPP1879
German Research Foundation (DFG)	Germany	SFB860

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release