6QUD | pdb_00006qud

2-deoxy-galactose reaction intermediate of a Truncated beta-galactosidase III from Bifidobacterium bifidum

• PDB DOI: https://doi.org/10.2210/pdb6QUD/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: 2.10 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 95.56 kDa 
• Atom Count: 7,139 
• Modeled Residue Count: 837 
• Deposited Residue Count: 885 
• Unique protein chains: 1

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2DG (Subject of Investigation/LOI)	B [auth A]	2-deoxy-alpha-D-galactopyranose C6 H12 O5 PMMURAAUARKVCB-ARQDHWQXSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.21	α = 90
b = 53.92	β = 106.59
c = 112.62	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: Derived calculations, Structure summary
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-11-13
  Changes: Structure summary