4XPQ

Crystal structure of Pedobacter saltans GH31 alpha-galactosidase complexed with L-fucose

• PDB DOI: https://doi.org/10.2210/pdb4XPQ/pdb

• Classification: HYDROLASE
• Organism(s): Pseudopedobacter saltans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-01-17 Released: 2015-05-20 
• Deposition Author(s): Miyazaki, T., Ishizaki, Y., Ichikawa, M., Nishikawa, A., Tonozuka, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.168 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 

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)

Macromolecule Content

• Total Structure Weight: 82.35 kDa 
• Atom Count: 6,027 
• Modelled Residue Count: 670 
• Deposited Residue Count: 720 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-glucosidase	A	720	Pseudopedobacter saltans	Mutation(s): 0  EC: 3.2.1.22
UniProt
Find proteins for A0A0F7R6D6 (Pseudopedobacter saltans) Explore A0A0F7R6D6  Go to UniProtKB:  A0A0F7R6D6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUL	C [auth A], D [auth A], E [auth A]	beta-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-KGJVWPDLSA-N
TRS	B [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.168 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.004	α = 90
b = 112.004	β = 90
c = 114.418	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-20 
Deposition Author(s): Miyazaki, T., Ishizaki, Y., Ichikawa, M., Nishikawa, A., Tonozuka, T.

Revision History  

• Version 1.0: 2015-05-20
  Type: Initial release
  
• Version 1.1: 2015-09-09
  Changes: Database references
• Version 1.2: 2020-02-05
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary