6R2Z | pdb_00006r2z

Aspergillus niger ferulic acid decarboxylase (Fdc) F437L variant in complex with the covalent adduct formed between prFMN cofactor and phenylpropiolic acid (Int1')

• PDB DOI: https://doi.org/10.2210/pdb6R2Z/pdb

• Classification: LYASE
• Organism(s): Aspergillus niger
• Expression System: Escherichia coli
• Mutation(s): Yes 


• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 
  0.153 (Depositor), 0.164 (DCC) 
• R-Value Work: 
  0.131 (Depositor) 
• R-Value Observed: 
  0.132 (Depositor) 

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: 57.11 kDa 
• Atom Count: 4,904 
• Modeled 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): 1  Gene Names: FDC1, ATCC64974_75990 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
JQZ (Subject of Investigation/LOI)	E [auth A]	prFMN cofactor and phenylpropiolic acid C31 H36 N4 O11 P ADKLHBNMILEONB-KSYXXAMZSA-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: 1.08 Å
• R-Value Free:  0.153 (Depositor), 0.164 (DCC) 
• R-Value Work:  0.131 (Depositor) 
• R-Value Observed: 0.132 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.734	α = 90
b = 64.133	β = 90
c = 87.574	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.

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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