8OED

Aspergillus niger ferulic acid decarboxylase (Fdc) S145C-P289C (DB2) variant in complex with prenylated flavin hydroxylated at the C1 prime position


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Aspergillus niger ferulic acid decarboxylase (Fdc) T40C-S315C (DB1) variant in complex with prenylated flavin hydroxylated at the C1 prime position

Roberts, G.W.Leys, D.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferulic acid decarboxylase 1508Aspergillus niger CBS 513.88Mutation(s): 2 
Gene Names: fdc1An03g06590
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2QHE5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BYN (Subject of Investigation/LOI)
Query on BYN

Download Ideal Coordinates CCD File 
B [auth A]hydroxylated prenyl-FMN
C22 H31 N4 O10 P
BDNVCRCOZIAGID-LWGWVAHUSA-N
SCN
Query on SCN

Download Ideal Coordinates CCD File 
F [auth A]THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
MN
Query on MN

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

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.879α = 90
b = 63.995β = 90
c = 87.708γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-06
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary