6R33

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

  • 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 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ferulic acid decarboxylase 1A508Aspergillus nigerMutation(s): 0 
Gene Names: fdc1An03g06590
EC: 4.1.1.102
UniProt
Find proteins for A2QHE5 (Aspergillus niger (strain CBS 513.88 / FGSC A1513))
Explore A2QHE5 
Go to UniProtKB:  A2QHE5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JQH
Query on JQH

Download Ideal Coordinates CCD File 
E [auth A]prFMN cofactor and phenylpropiolic acid adduct
C30 H35 N4 O9 P
PESIXFCXBGLILZ-QNFINUSWSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
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 = 95.89α = 90
b = 64.21β = 90
c = 87.57γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-03-19 
  • Released Date: 2019-08-28 
  • Deposition Author(s): Bailey, S.S., Leys, D.

Funding OrganizationLocationGrant Number
European Research CouncilUnited KingdompreFAB 695013
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K017802

Revision History  (Full details and data files)

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