6R33

Aspergillus niger ferulic acid decarboxylase (Fdc)in complex with the covalent adduct formed between prFMN cofactor and phenylpropiolic acid, following decarboxylation (Int3')

• PDB DOI:  https://doi.org/10.2210/pdb6R33/pdb

• Classification: LYASE
• Organism(s): Aspergillus niger
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-03-19 Released: 2019-08-28 
• Deposition Author(s): Bailey, S.S., Leys, D.
• Funding Organization(s): European Research Council, Biotechnology and Biological Sciences Research Council

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.01 Å
• R-Value Free: 0.136 
• R-Value Work: 0.117 
• R-Value Observed: 0.118 

Literature

Atomic description of an enzyme reaction dependent on reversible 1,3-dipolar cycloaddition

Bailey, S.S., Payne, K.A.P., Saaret, A., Marshall, S.A., Gostimskaya, I., Kosov, I., Fisher, K., Hay, S., Leys, D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 57.1 kDa 
• Atom Count: 4,946 
• Modelled Residue Count: 500 
• Deposited Residue Count: 508 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferulic acid decarboxylase 1	A	508	Aspergillus niger	Mutation(s): 0  Gene Names: fdc1, An03g06590 EC: 4.1.1.102
UniProt
Find proteins for A2QHE5 (Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513)) Explore A2QHE5  Go to UniProtKB:  A2QHE5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JQH (Subject of Investigation/LOI)	E [auth A]	prFMN cofactor and phenylpropiolic acid adduct C30 H35 N4 O9 P PESIXFCXBGLILZ-QNFINUSWSA-N
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
K	C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.01 Å
• R-Value Free: 0.136 
• R-Value Work: 0.117 
• R-Value Observed: 0.118 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.89	α = 90
b = 64.21	β = 90
c = 87.57	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-28 
Deposition Author(s): Bailey, S.S., Leys, D.

---

Funding Organization	Location	Grant Number
European Research Council	United Kingdom	preFAB 695013
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/K017802

Revision History  

• Version 1.0: 2019-08-28
  Type: Initial release