9GJ0

Eugenol Oxidase (EUGO) from Rhodococcus jostii RHA1, mutant B1

PDB DOI: https://doi.org/10.2210/pdb9GJ0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhodococcus jostii RHA1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-08-20 Released: 2024-12-18
Deposition Author(s): Rozeboom, H.J., Fraaije, M.W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free:
0.266 (Depositor), 0.257 (DCC)
R-Value Work:
0.206 (Depositor), 0.206 (DCC)
R-Value Observed:
0.209 (Depositor)

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

Biocatalytic Cleavage of para-Acetoxy Benzyl Ethers: Application to Protecting Group Chemistry

Ashley, B., Demingo, C., Rozeboom, H., Bianciardi, N., Dunleavy, T., Haaksma, J.J., Guo, Y., Fraaije, M.W.

(2025) ACS Catal 15: 105-113

DOI: https://doi.org/10.1021/acscatal.4c04257

Macromolecule Content

Total Structure Weight: 186.82 kDa
Atom Count: 12,362
Modelled Residue Count: 1,559
Deposited Residue Count: 1,656
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable vanillyl-alcohol oxidase	A, B, C	552	Rhodococcus jostii RHA1	Mutation(s): 11 Gene Names: RHA1_ro03282 EC: 1.1.3.38
UniProt
Find proteins for Q0SBK1 (Rhodococcus jostii (strain RHA1)) Explore Q0SBK1 Go to UniProtKB: Q0SBK1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0SBK1
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free: 0.266 (Depositor), 0.257 (DCC)
R-Value Work: 0.206 (Depositor), 0.206 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.77	α = 90
b = 109.77	β = 90
c = 244.985	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-12-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-12-18
Type: Initial release
Version 1.1: 2025-01-29
Changes: 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.