6SE9

Cold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB mutant E441Q in complex with lactose bound in shallow mode

• PDB DOI: https://doi.org/10.2210/pdb6SE9/pdb

• Classification: HYDROLASE
• Organism(s): Arthrobacter sp. 32cB
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-07-29 Released: 2019-09-11 
• Deposition Author(s): Rutkiewicz, M., Bujacz, A., Bujacz, G.
• Funding Organization(s): Polish National Science Centre

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.238 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 

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: 110.96 kDa 
• Atom Count: 8,098 
• Modelled Residue Count: 989 
• Deposited Residue Count: 1,010 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A	1,010	Arthrobacter sp. 32cB	Mutation(s): 1  EC: 3.2.1.23
UniProt
Find proteins for A0A023UGN9 (Arthrobacter sp. 32cB) Explore A0A023UGN9  Go to UniProtKB:  A0A023UGN9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G84224TW GlyCosmos:  G84224TW GlyGen:  G84224TW

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GAL (Subject of Investigation/LOI)	K [auth A]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
FRU (Subject of Investigation/LOI)	I [auth A], J [auth A]	beta-D-fructofuranose C6 H12 O6 RFSUNEUAIZKAJO-ARQDHWQXSA-N
MLI	G [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
ACT	E [auth A], F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT	H [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004	B	beta-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.238 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.902	α = 90
b = 138.902	β = 90
c = 127.875	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Rutkiewicz, M., Bujacz, A., Bujacz, G.

---

Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2016/21/B/ST5/00555

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2019-09-18
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary