8U09

Crystal structure of substrate-free SyoA

• PDB DOI: https://doi.org/10.2210/pdb8U09/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Amycolatopsis thermoflava N1165
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-08-28 Released: 2024-07-24 
• Deposition Author(s): Harlington, A.H., Shearwin, K.E., Bell, S.G., Whelan, F.
• Funding Organization(s): Wine Australia

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.205 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Starting Model: in silico

Literature

Structural insights into the S-lignin O-demethylase SyoA

Harlington, A.H., Shearwin, K.E., Bell, S.G., Whelan, F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.76 kDa 
• Atom Count: 3,511 
• Modelled Residue Count: 392 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A	412	Amycolatopsis thermoflava N1165	Mutation(s): 0  EC: 1.14.14.1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
GOL	C [auth A], D [auth A], E [auth A], F [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.205 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M38U09

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.86	α = 90
b = 150.242	β = 90
c = 60.642	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-24 
Deposition Author(s): Harlington, A.H., Shearwin, K.E., Bell, S.G., Whelan, F.

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Funding Organization	Location	Grant Number
Wine Australia	Australia	PH2002

Revision History  

• Version 1.0: 2024-07-24
  Type: Initial release