6R2P

Aspergillus niger ferulic acid decarboxylase (Fdc) in complex with FMN and cinnamic acid

• PDB DOI: https://doi.org/10.2210/pdb6R2P/pdb

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


• Deposited: 2019-03-18 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: 1.26 Å
• R-Value Free: 0.187 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 

Starting Model: experimental

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 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 57.07 kDa 
• Atom Count: 4,552 
• Modelled Residue Count: 497 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN (Subject of Investigation/LOI)	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
TCA (Subject of Investigation/LOI)	F [auth A]	PHENYLETHYLENECARBOXYLIC ACID C9 H8 O2 WBYWAXJHAXSJNI-VOTSOKGWSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
K	D [auth A], E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 0.187 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.895	α = 90
b = 63.835	β = 90
c = 87.651	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	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
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description