8U7F

Crystal structure of CIB_12 beta-galactosidase from Cuniculiplasma divulgatum

• PDB DOI: https://doi.org/10.2210/pdb8U7F/pdb

• Classification: HYDROLASE
• Organism(s): Cuniculiplasma divulgatum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-09-15 Released: 2024-07-24 
• Deposition Author(s): Stogios, P.J., Skarina, T., Di Leo, R., Yakunin, A., Golyshin, P., Savchenko, A.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.260 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 

Starting Model: experimental

Literature

Crystal structure of CIB_12 beta-galactosidase from Cuniculiplasma divulgatum

Stogios, P.J.

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: 113.97 kDa 
• Atom Count: 8,043 
• Modelled Residue Count: 955 
• Deposited Residue Count: 968 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CIB_12 Beta-galactosidase	A, B	484	Cuniculiplasma divulgatum	Mutation(s): 0  Gene Names: CSP5_0942
UniProt
Find proteins for A0A1N5UH46 (Cuniculiplasma divulgatum) Explore A0A1N5UH46  Go to UniProtKB:  A0A1N5UH46

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.260 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.215	α = 90
b = 51.805	β = 108.34
c = 128.794	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-24 
Deposition Author(s): Stogios, P.J., Skarina, T., Di Leo, R., Yakunin, A., Golyshin, P., Savchenko, A.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-07-24
  Type: Initial release