6V43

Crystal structure of the flavin oxygenase with cofactor and substrate bound involved in folate catabolism

• PDB DOI: https://doi.org/10.2210/pdb6V43/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Hoeflea phototrophica DFL-43
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-11-27 Released: 2020-12-09 
• Deposition Author(s): Begley, T.P., Adak, S., Zhao, B., Li, P.
• Funding Organization(s): Robert A. Welch Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.202 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 

Starting Model: experimental

Literature

A novel flavoenzyme catalyzed Baeyer-Villiger type rearrangement in bacterial folic acid catabolic pathway

Begley, T.P., Adak, S., Zhao, B., Li, P.

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: 106.72 kDa 
• Atom Count: 8,537 
• Modelled Residue Count: 932 
• Deposited Residue Count: 934 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAD/FMN-containing dehydrogenase	A, B	467	Hoeflea phototrophica DFL-43	Mutation(s): 0  Gene Names: HPDFL43_08194
UniProt
Find proteins for A9D9D1 (Hoeflea phototrophica (strain DSM 17068 / NCIMB 14078 / DFL-43)) Explore A9D9D1  Go to UniProtKB:  A9D9D1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	D [auth A], F [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
LUZ (Subject of Investigation/LOI)	C [auth A], E [auth B]	pteridine-2,4(1H,3H)-dione C6 H4 N4 O2 UYEUUXMDVNYCAM-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.202 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.56	α = 90
b = 125.38	β = 90
c = 127.31	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): Begley, T.P., Adak, S., Zhao, B., Li, P.

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Funding Organization	Location	Grant Number
Robert A. Welch Foundation	United States	A0034

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-10-09
  Changes: Structure summary