6WTA

Structure of F420-H2 Dependent Oxidoreductase (FDOR-A) MSMEG_2027 in complex with F420

PDB DOI: https://doi.org/10.2210/pdb6WTA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycolicibacterium smegmatis MC2 155
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-05-01 Released: 2021-05-05
Deposition Author(s): Jackson, C.J., Antoney, J.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.241
R-Value Work: 0.200
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

A F420-dependent single domain chemogenetic tool for protein de-dimerization

Antoney, J., Kainrath, S., Ahmed, F.H., Kang, S.W., Mackie, E.R., Soares da Costa, T.P., Jackson, C.J., Janovjak, H.

(2022) Biorxiv

DOI: https://doi.org/10.1101/2022.11.07.515376

Macromolecule Content

Total Structure Weight: 33.09 kDa
Atom Count: 1,337
Modelled Residue Count: 143
Deposited Residue Count: 280
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B [auth Z]	140	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: MSMEG_2027
UniProt
Find proteins for A0QU01 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QU01 Go to UniProtKB: A0QU01
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QU01
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UBM (Subject of Investigation/LOI) Query on UBM Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	COENZYME F420-4 C₃₉ H₅₀ N₇ O₂₄ P HYGZFZXLFYAPGM-DKJXVAHLSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.241
R-Value Work: 0.200
R-Value Observed: 0.202
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.364	α = 90
b = 63.022	β = 90
c = 65.366	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-05-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-05-05
Type: Initial release
Version 1.1: 2022-11-16
Changes: Database references
Version 1.2: 2023-10-18
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.