8U7G

Crystal structure of CIB_13 beta-galactosidase from Cuniculiplasma divulgatum

• PDB DOI: https://doi.org/10.2210/pdb8U7G/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.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.219 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

Crystal structure of CIB_13 beta-galactosidase from Cuniculiplasma divulgatum

Stogios, P.J., Skarina, T., Di Leo, R., Yakunin, A., Golyshin, P.

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: 112.75 kDa 
• Atom Count: 8,628 
• Modelled Residue Count: 964 
• Deposited Residue Count: 964 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CIB_13 Beta-galactosidase	A, B	482	Cuniculiplasma divulgatum	Mutation(s): 0  Gene Names: CSP5_1651
UniProt
Find proteins for A0A1N5W3X4 (Cuniculiplasma divulgatum) Explore A0A1N5W3X4  Go to UniProtKB:  A0A1N5W3X4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	D [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.219 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.8	α = 90
b = 102.188	β = 104.69
c = 97.542	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.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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