2GFT | pdb_00002gft

Crystal structure of the E263A nucleophile mutant of Bacillus licheniformis endo-beta-1,4-galactanase in complex with galactotriose

• PDB DOI: https://doi.org/10.2210/pdb2GFT/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus licheniformis
• Expression System: Bacillus subtilis
• Mutation(s): Yes 


• Deposited: 2006-03-23 Released: 2006-06-13 
• Deposition Author(s): Welner, D., Le Nours, J., De Maria, L., 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: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

Oligosaccharide binding of Bacillus licheniformis endo-beta-1,4-galactanase

Le Nours, J., De Maria, L., Welner, D., Jorgensen, C.T., Christensen, L.L.H., Larsen, S., Lo Leggio, L.

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: 88.53 kDa 
• Atom Count: 6,361 
• Modeled Residue Count: 773 
• Deposited Residue Count: 798 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl Hydrolase Family 53	A, B	399	Bacillus licheniformis	Mutation(s): 1  EC: 3.2.1.89 (PDB Primary Data), 3.2.1 (UniProt)
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	D Interactions
beta-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose	C, D	3		N/A
Glycosylation Resources
GlyTouCan: G06996VN GlyCosmos: G06996VN GlyGen: G06996VN

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.273	α = 90
b = 79.354	β = 100.56
c = 103.906	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-13 
Deposition Author(s): Welner, D., Le Nours, J., De Maria, L., Jorgensen, C.T., Christensen, L.L.H., Larsen, S., Lo Leggio, L.

Revision History  

• Version 1.0: 2006-06-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-24
  Changes: Data collection, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2021-10-20
  Changes: Database references, Structure summary
• Version 2.2: 2024-02-14
  Changes: Data collection, Refinement description