8OFG

Streptococcus pneumoniae CdaA in complex with c-di-amp

• PDB DOI: https://doi.org/10.2210/pdb8OFG/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus pneumoniae R6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-03-15 Released: 2023-06-21 
• Deposition Author(s): Garbers, T.B., Neumann, P., Ficner, R.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.252 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 

Literature

Streptococcus pneumoniae CdaA in complex with c-di-amp

Garbers, T.B., Neumann, P., Ficner, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 41.57 kDa 
• Atom Count: 2,462 
• Modelled Residue Count: 309 
• Deposited Residue Count: 370 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diadenylate cyclase	A, B	181	Streptococcus pneumoniae R6	Mutation(s): 0  Gene Names: dacA
UniProt
Find proteins for Q8DP14 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DP14  Go to UniProtKB:  Q8DP14

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLU-ARG-LEU-LEU-GLY-GLY-TRP-LYS	C	8	Streptococcus pneumoniae R6	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP (Subject of Investigation/LOI)	D [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.252 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.57	α = 90
b = 86.57	β = 90
c = 110.62	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-21 
Deposition Author(s): Garbers, T.B., Neumann, P., Ficner, R.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SPP 1879

Revision History  

• Version 1.0: 2023-06-21
  Type: Initial release