8OGK | pdb_00008ogk

Crystal structure of CdaA from Bacillus subtilis co-crystallized with DMSO

• PDB DOI: https://doi.org/10.2210/pdb8OGK/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-03-20 Released: 2024-03-27 
• 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: 1.18 Å
• R-Value Free: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Crystal structure of CdaA from Bacillus subtilis co-crystallized with DMSO

Garbers, T.B., Neumann, P., Wollenhaupt, J., Weiss, M., Ficner, R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.7 kDa 
• Atom Count: 2,516 
• Modeled Residue Count: 304 
• Deposited Residue Count: 308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic di-AMP synthase CdaA	A, B	154	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: cdaA, ybbP, BSU01750 EC: 2.7.7.85
UniProt
Find proteins for Q45589 (Bacillus subtilis (strain 168)) Explore Q45589  Go to UniProtKB:  Q45589

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DMS	C [auth A], D [auth A], E [auth A], G [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.65	α = 90
b = 39.24	β = 94.99
c = 67.98	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: 2024-03-27 
Deposition Author(s): Garbers, T.B., Neumann, P., Ficner, R.

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

Revision History  

• Version 1.0: 2024-03-27
  Type: Initial release