6ZZA

Crystal structure of CbpB in complex with c-di-AMP

• PDB DOI: https://doi.org/10.2210/pdb6ZZA/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Streptococcus agalactiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-08-04 Released: 2021-08-18 
• Deposition Author(s): Mechaly, A.E., Covaleda-Cortes, G., Kaminski, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.245 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

Starting Model: experimental

Literature

Crystal structure of CbpB in complex with c-di-AMP

Mechaly, A.E., Covaleda-Cortes, G., Kaminski, P.A.

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 20.6 kDa 
• Atom Count: 1,288 
• Modelled Residue Count: 150 
• Deposited Residue Count: 176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CBS domain-containing protein	A	176	Streptococcus agalactiae	Mutation(s): 0  Gene Names: ykuL, C6N06_01440, D5F95_08070, DX05_08405, E8E04_03435, F5F86_02645, NCTC9828_00932, WA02_02795, WA05_04310
UniProt
Find proteins for A0A076YWK5 (Streptococcus agalactiae) Explore A0A076YWK5  Go to UniProtKB:  A0A076YWK5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2BA (Subject of Investigation/LOI)	B [auth A]	(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide C20 H24 N10 O12 P2 PDXMFTWFFKBFIN-XPWFQUROSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.245 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.83	α = 90
b = 93.83	β = 90
c = 33.6	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
PHASER	phasing
Aimless	data scaling
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-08-18 
Deposition Author(s): Mechaly, A.E., Covaleda-Cortes, G., Kaminski, P.A.

Revision History  

• Version 1.0: 2021-08-18
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description