6QUB | pdb_00006qub

Truncated beta-galactosidase III from Bifidobacterium bifidum in complex with galactose

• PDB DOI: https://doi.org/10.2210/pdb6QUB/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Bifidobacterium bifidum
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 2019-02-27 Released: 2020-03-18 
• Deposition Author(s): Thirup, S.S., Nielsen, J.A., Andersen, J.L., Alsarraf, H., Blaise, M.
• Funding Organization(s): Danish Agency for Science Technology and Innovation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Truncated beta-galactosidase III from Bifidobacterium bifidum

Nielsen, J.A., Andersen, J.L., Alsarraf, H., Blaise, M., Thirup, S.S., Larsen, M.K., Cramer, J.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 188.3 kDa 
• Atom Count: 15,669 
• Modelled Residue Count: 1,714 
• Deposited Residue Count: 1,742 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A	885	Bifidobacterium bifidum	Mutation(s): 0  EC: 3.2.1.23
UniProt
Find proteins for Q9F4D5 (Bifidobacterium bifidum) Explore Q9F4D5  Go to UniProtKB:  Q9F4D5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	B	857	Bifidobacterium bifidum	Mutation(s): 0  EC: 3.2.1.23
UniProt
Find proteins for Q9F4D5 (Bifidobacterium bifidum) Explore Q9F4D5  Go to UniProtKB:  Q9F4D5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GAL	C [auth A], F [auth B]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
CA	D [auth A], E [auth A], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.781	α = 90
b = 54.592	β = 107.72
c = 143.357	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Thirup, S.S., Nielsen, J.A., Andersen, J.L., Alsarraf, H., Blaise, M.

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Funding Organization	Location	Grant Number
Danish Agency for Science Technology and Innovation	Denmark	--

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Refinement description, Structure summary
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references, Structure summary