8OHO

PanDDA analysis group deposition -- CdaA in complex with fragment F2X-Entry H11

• PDB DOI: https://doi.org/10.2210/pdb8OHO/pdb

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


• Deposited: 2023-03-21 Released: 2024-04-03 
• Deposition Author(s): Garbers, T.B., Neumann, P., Wollenhaupt, J., Weiss, M.S., Ficner, R.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 0.225 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Literature

PanDDA analysis group deposition -- CdaA in complex with fragment F2X-Entry H11

Garbers, T.B., Neumann, P., Wollenhaupt, J., Weiss, M.S., 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: 33.81 kDa 
• Atom Count: 2,497 
• Modelled Residue Count: 299 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
REG	D [auth B]	1-cyclopentyl-3-[[(2~{S})-oxolan-2-yl]methyl]urea C11 H20 N2 O2 GZCFMEFTVSKHDE-JTQLQIEISA-N
TBJ (Subject of Investigation/LOI)	C [auth A]	N-cyclopentyl-N'-{[(2R)-oxolan-2-yl]methyl}urea C11 H20 N2 O2 GZCFMEFTVSKHDE-SNVBAGLBSA-N
MG	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 0.225 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.7	α = 90
b = 39.33	β = 95.28
c = 68.11	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: 2024-04-03 
Deposition Author(s): Garbers, T.B., Neumann, P., Wollenhaupt, J., Weiss, M.S., Ficner, R.

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

Revision History  

• Version 1.0: 2024-04-03
  Type: Initial release