6MOT | pdb_00006mot

Bacteroides intestinalis feruloyl esterase, Bacint_01033

• PDB DOI: https://doi.org/10.2210/pdb6MOT/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides intestinalis DSM 17393
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-04 Released: 2019-10-16 
• Deposition Author(s): Koropatkin, N.M., Pereira, G.V., Cann, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.191 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Degradation of complex arabinoxylans by human colonic Bacteroidetes

Pereira, G.V., DAlessandro-Gabazza, C., Farris, J., Wefers, D., Mackie, R., Koropatkin, N.M., Gabazza, E.C., Cann, I.

(2021) Nat Commun 

• DOI: https://doi.org/10.1038/s41467-020-20737-5

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.35 kDa 
• Atom Count: 3,080 
• Modeled Residue Count: 345 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoamylase N-terminal domain protein	A	360	Bacteroides intestinalis DSM 17393	Mutation(s): 0  Gene Names: BACINT_01033
UniProt
Find proteins for B3C969 (Bacteroides intestinalis DSM 17393) Explore B3C969  Go to UniProtKB:  B3C969

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.191 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.959	α = 90
b = 99.959	β = 90
c = 164.204	γ = 120

Software Package:

Software Name	Purpose
xia2	data scaling
SOLVE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-16 
Deposition Author(s): Koropatkin, N.M., Pereira, G.V., Cann, I.

Revision History  

• Version 1.0: 2019-10-16
  Type: Initial release
  
• Version 1.1: 2021-01-27
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Structure summary