6V42

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

PDB DOI: https://doi.org/10.2210/pdb6V42/pdb

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

Deposited: 2019-11-27 Released: 2020-12-02
Deposition Author(s): Begley, T.P., Adak, S., Zhao, B., Li, P.
Funding Organization(s): Robert A. Welch Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.175
R-Value Work: 0.152
R-Value Observed: 0.153

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 106.4 kDa
Atom Count: 8,507
Modelled Residue Count: 932
Deposited Residue Count: 934
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9D9D1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.175
R-Value Work: 0.152
R-Value Observed: 0.153
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.669	α = 90
b = 125.209	β = 90
c = 127.329	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-12-02

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2020-12-02
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.