7KV3

Surface glycan-binding protein A from Bacteroides thetaiotaomicron in complex with laminarihexaose

• PDB DOI: https://doi.org/10.2210/pdb7KV3/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Bacteroides thetaiotaomicron
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-11-26 Released: 2021-02-17 
• Deposition Author(s): Tamura, K., Brumer, H., Van Petegem, F.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.204 
• R-Value Work: 0.157 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 60.44 kDa 
• Atom Count: 4,160 
• Modelled Residue Count: 467 
• Deposited Residue Count: 515 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RagB/SusD family nutrient uptake outer membrane protein	A [auth AAA]	515	Bacteroides thetaiotaomicron	Mutation(s): 0  Gene Names: DW011_12550, DW780_14665, DWY18_18425, GAN67_20195, GAN98_19115
UniProt
Find proteins for A0A173VPY3 (Bacteroides thetaiotaomicron) Explore A0A173VPY3  Go to UniProtKB:  A0A173VPY3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	B [auth AaA]	6		N/A
Glycosylation Resources
GlyTouCan:  G41202OE GlyCosmos:  G41202OE GlyGen:  G41202OE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth AAA]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900020	B [auth AaA]	beta-cellohexaose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.204 
• R-Value Work: 0.157 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.024	α = 90
b = 72.937	β = 105.644
c = 101.484	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Tamura, K., Brumer, H., Van Petegem, F.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release
  
• Version 1.1: 2021-03-03
  Changes: Database references
• Version 1.2: 2021-07-21
  Changes: Database references
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references