6JHP | pdb_00006jhp

Crystal structure of the glycoside hydrolase family 36 alpha-galactosidase from Paecilomyces thermophila

• PDB DOI: https://doi.org/10.2210/pdb6JHP/pdb

• Classification: HYDROLASE
• Organism(s): Paecilomyces sp. 'thermophila
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-02-18 Released: 2020-05-20 
• Deposition Author(s): Liu, Y., Huang, P., Ma, J., Jiang, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Crystal structure and phylogenetic analysis of the glycoside hydrolase family 36 alpha-galactosidase from Paecilomyces thermophila

Liu, Y., Huang, P., Ma, J., Jiang, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 336.09 kDa 
• Atom Count: 22,793 
• Modeled Residue Count: 2,864 
• Deposited Residue Count: 3,032 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-galactosidase	A, B, C, D	758	Paecilomyces sp. 'thermophila	Mutation(s): 0  EC: 3.2.1.22
UniProt
Find proteins for A0A2Z4HIN9 (Paecilomyces sp. 'thermophila') Explore A0A2Z4HIN9  Go to UniProtKB:  A0A2Z4HIN9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	E [auth A], F [auth A], G [auth B], H [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.25	α = 90
b = 173.043	β = 90
c = 177.277	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-20 
Deposition Author(s): Liu, Y., Huang, P., Ma, J., Jiang, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2020-05-20
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description