6CA3 | pdb_00006ca3

THE CRYSTAL STRUCTURE OF THE W169Y MUTANT OF ALPHA-GLUCOSIDASE (GH 31) FROM RUMINOCOCCUS OBEUM ATCC 29174 in complex with miglitol

• PDB DOI: https://doi.org/10.2210/pdb6CA3/pdb

• Classification: HYDROLASE
• Organism(s): Blautia obeum ATCC 29174
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-01-29 Released: 2018-02-28 
• Deposition Author(s): Tan, K., Tesar, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Macromolecular Research (MCMR)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

THE CRYSTAL STRUCTURE OF THE W169Y MUTANT OF ALPHA-GLUCOSIDASE (GH 31) FROM RUMINOCOCCUS OBEUM ATCC 29174 in complex with miglitol

Tan, K., Tesar, C., Jedrzejczak, R., Joachimiak, A.

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.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 155.36 kDa 
• Atom Count: 11,920 
• Modeled Residue Count: 1,331 
• Deposited Residue Count: 1,332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase, family 31	A, B	666	Blautia obeum ATCC 29174	Mutation(s): 1  Gene Names: RUMOBE_03919 EC: 3.2.1
UniProt
Find proteins for A5ZY13 (Blautia obeum ATCC 29174) Explore A5ZY13  Go to UniProtKB:  A5ZY13

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MIG	C [auth A], E [auth B]	(2R,3R,4R,5S)-1-(2-hydroxyethyl)-2-(hydroxymethyl)piperidine-3,4,5-triol C8 H17 N O5 IBAQFPQHRJAVAV-ULAWRXDQSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.685	α = 111.32
b = 70.826	β = 107.42
c = 88.103	γ = 97.66

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): Tan, K., Tesar, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Macromolecular Research (MCMR)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094585
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115586

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release
  
• Version 1.1: 2021-07-21
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description