7BLJ | pdb_00007blj

Structure of CBM BT3015C from Bacteroides thetaiotaomicron in complex with O-GalNAc core 2-Thr

• PDB DOI: https://doi.org/10.2210/pdb7BLJ/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2021-01-18 Released: 2022-03-02 
• Deposition Author(s): Costa, R.L.
• Funding Organization(s): Foundation for Science and Technology (FCT)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Structural basis for mucin-type O-glycan recognition by proteins of a Bacteroides thetaiotaomicron polysaccharide utilization loci

Costa, R.L., Correia, V.G.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 18.73 kDa 
• Atom Count: 1,398 
• Modeled Residue Count: 142 
• Deposited Residue Count: 162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
family 32 carbohydrate-binding module from Bacteroides thetaiotaomicron	A	162	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  Gene Names: BT_3015
UniProt
Find proteins for Q8A3D9 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A3D9  Go to UniProtKB:  Q8A3D9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-galactopyranose	B	3		O-Glycosylation
Glycosylation Resources
GlyTouCan:  G00033MO GlyCosmos:  G00033MO GlyGen:  G00033MO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
THR (Subject of Investigation/LOI)	D [auth A]	THREONINE C4 H9 N O3 AYFVYJQAPQTCCC-GBXIJSLDSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.541	α = 90
b = 64.965	β = 90
c = 70.603	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SAINT	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Costa, R.L.

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Funding Organization	Location	Grant Number
Foundation for Science and Technology (FCT)	Portugal	PTDC/BIA-MIB/31730/2017

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description