3PHA | pdb_00003pha

The crystal structure of the W169Y mutant of alpha-glucosidase (gh31 family) from Ruminococcus obeum atcc 29174 in complex with acarbose

• PDB DOI: https://doi.org/10.2210/pdb3PHA/pdb
• Entry: 3PHA supersedes: 3NXM

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Blautia obeum ATCC 29174
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-11-03 Released: 2010-11-24 
• Deposition Author(s): Tan, K., Tesar, C., Keigher, L., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.265 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of the W169Y mutant of alpha-glucosidase (gh31 family) from Ruminococcus obeum atcc 29174 in complex with acarbose

Tan, K., Tesar, C., Keigher, L., Babnigg, G., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 312.29 kDa 
• Atom Count: 22,569 
• Modeled Residue Count: 2,660 
• Deposited Residue Count: 2,664 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha-glucosidase	A, B, C, D	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

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	E, F, G, H	3	N/A	N/A
Glycosylation Resources
GlyTouCan: G66431MI GlyCosmos: G66431MI

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900007	E, F, G, H	alpha-acarbose	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.265 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.032	α = 90
b = 125.955	β = 107.72
c = 133.58	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-24 
Deposition Author(s): Tan, K., Tesar, C., Keigher, L., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• This entry supersedes: 3NXM

Revision History  

• Version 1.0: 2010-11-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2017-07-19
  Changes: Advisory, Database references, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 3.1: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary