5C70 | pdb_00005c70

The structure of Aspergillus oryzae beta-glucuronidase

• PDB DOI: https://doi.org/10.2210/pdb5C70/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus oryzae
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2015-06-24 Released: 2016-06-15 
• Deposition Author(s): Sun, H.L., Lv, B., Huang, S., Sun, Q.F., Li, C., Jiang, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Enhancing the Thermostability of beta-Glucuronidase by Rationally Redesigning the Catalytic Domain Based on Sequence Alignment Strategy

Feng, X.D., Tang, H., Han, B.J., Lv, B., Li, C.

(2016) Ind Eng Chem Res 55: 5474-5483

• DOI: https://doi.org/10.1021/acs.iecr.6b00535

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)

Macromolecule Content 

• Total Structure Weight: 136.96 kDa 
• Atom Count: 9,320 
• Modeled Residue Count: 1,172 
• Deposited Residue Count: 1,224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucuronidase	A, B	612	Aspergillus oryzae	Mutation(s): 0  Gene Names: Pgus EC: 3.2.1.25 (PDB Primary Data), 3.2.1.31 (UniProt)
UniProt
Find proteins for A7XS03 (Aspergillus oryzae) Explore A7XS03  Go to UniProtKB:  A7XS03

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.32	α = 90
b = 110.32	β = 90
c = 480.722	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data processing
HKL-2000	data scaling
AMoRE	phasing
REFMAC	refinement
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-15 
Deposition Author(s): Sun, H.L., Lv, B., Huang, S., Sun, Q.F., Li, C., Jiang, T.

Revision History  

• Version 1.0: 2016-06-15
  Type: Initial release
  
• Version 1.1: 2023-03-01
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2024-05-29
  Changes: Data collection