2CCR

Structure of Beta-1,4-Galactanase

• PDB DOI: https://doi.org/10.2210/pdb2CCR/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus licheniformis
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 2006-01-18 Released: 2006-03-21 
• Deposition Author(s): Le Nours, J., De Maria, L., Welner, D., Jorgensen, C.T., Christensen, L.L.H., Larsen, S., Lo Leggio, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.245 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 89.63 kDa 
• Atom Count: 6,297 
• Modelled Residue Count: 775 
• Deposited Residue Count: 798 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YVFO	A, B	399	Bacillus licheniformis	Mutation(s): 0  EC: 3.2.1.89
UniProt
Find proteins for Q65CX5 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)) Explore Q65CX5  Go to UniProtKB:  Q65CX5

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose	C, E	3		N/A
Glycosylation Resources
GlyTouCan:  G06996VN GlyCosmos:  G06996VN GlyGen:  G06996VN

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-galactopyranose	D, F	2		N/A
Glycosylation Resources
GlyTouCan:  G08806VI GlyCosmos:  G08806VI GlyGen:  G08806VI

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	H [auth B], I [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CA	G [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900114	C, E	4beta-beta-galactotriose	Oligosaccharide / Metabolism

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900113	D, F	4beta-beta-galactobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.245 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.37	α = 90
b = 80.64	β = 99.29
c = 104.44	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-21 
Deposition Author(s): Le Nours, J., De Maria, L., Welner, D., Jorgensen, C.T., Christensen, L.L.H., Larsen, S., Lo Leggio, L.

Revision History  

• Version 1.0: 2006-03-21
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-17
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary