9GJ0 | pdb_00009gj0

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), 0.242 (DCC)
R-Value Work:
0.206 (Depositor)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 1,559
Deposited Residue Count: 1,656
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.242 (DCC)
R-Value Work: 0.206 (Depositor)
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

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.