7WJR

Crystal structure of dihydroxybenzoate decarboxylase mutant A63S from Aspergillus oryzae in complex with catechol

• PDB DOI: https://doi.org/10.2210/pdb7WJR/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus oryzae RIB40
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-01-07 Released: 2023-01-18 
• Deposition Author(s): Yan, F., Song, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.175 
• R-Value Work: 0.144 
• R-Value Observed: 0.144 

Literature

Molecular mechanism of reversible decarboxylase with efficient CO2 fixation

Yan, F., Song, X.

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: 156.78 kDa 
• Atom Count: 12,806 
• Modelled Residue Count: 1,356 
• Deposited Residue Count: 1,356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,3-dihydroxybenzoate decarboxylase	A, B, C, D	339	Aspergillus oryzae RIB40	Mutation(s): 1  EC: 4.1.1.46
UniProt
Find proteins for P80402 (Aspergillus oryzae (strain ATCC 42149 / RIB 40)) Explore P80402  Go to UniProtKB:  P80402

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAQ (Subject of Investigation/LOI)	F [auth A], H [auth B], J [auth C], L [auth D]	CATECHOL C6 H6 O2 YCIMNLLNPGFGHC-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C], K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.175 
• R-Value Work: 0.144 
• R-Value Observed: 0.144 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.932	α = 90
b = 105.842	β = 90
c = 181.689	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Yan, F., Song, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21877110

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description