6QUC | pdb_00006quc

Truncated beta-galactosidase III from Bifidobacterium bifidum

• PDB DOI: https://doi.org/10.2210/pdb6QUC/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: 2.30 Å
• R-Value Free: 
  0.218 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (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 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: 191.29 kDa 
• Atom Count: 13,892 
• Modeled Residue Count: 1,718 
• Deposited Residue Count: 1,770 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A, B	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
IMD	E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CA	C [auth A], D [auth A], H [auth B], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.218 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.5	α = 90
b = 119.683	β = 90
c = 144.602	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: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description