7SNK

Structure of Bacple_01702, a GH29 family glycoside hydrolase

• PDB DOI: https://doi.org/10.2210/pdb7SNK/pdb

• Classification: HYDROLASE
• Organism(s): Phocaeicola plebeius DSM 17135
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2021-10-28 Released: 2022-10-05 
• Deposition Author(s): Ulaganathan, T., Cygler, M.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.214 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Starting Model: experimental

Literature

The porphyran degradation system of the human gut microbiota is complete, phylogenetically diverse and geographically structured across Asian populations

Mathieu, S., Touvrey, M., Poulet, L., Drouillard, S., Ulaganathan, T.S., Segurel, L., Cygler, M., Helbert, W.

(2023) bioRxiv 

• DOI: https://doi.org/10.1101/2023.03.30.534863

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: 68.27 kDa 
• Atom Count: 4,970 
• Modelled Residue Count: 564 
• Deposited Residue Count: 597 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-L-fucosidase	A	597	Phocaeicola plebeius DSM 17135	Mutation(s): 0  Gene Names: BACPLE_01702
UniProt
Find proteins for B5CYA5 (Phocaeicola plebeius (strain DSM 17135 / JCM 12973 / CCUG 54634 / M2)) Explore B5CYA5  Go to UniProtKB:  B5CYA5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.214 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.45	α = 90
b = 77.43	β = 90
c = 133.79	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
Coot	model building
autoPROC	data reduction
autoPROC	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-05 
Deposition Author(s): Ulaganathan, T., Cygler, M.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History  

• Version 1.0: 2022-10-05
  Type: Initial release
  
• Version 1.1: 2023-05-10
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description