9LP3 | pdb_00009lp3

Crystal structure of Aromatic Dioxygenase CpuAdo(Coniochaeta pulveracea)

• PDB DOI: https://doi.org/10.2210/pdb9LP3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Coniochaeta pulveracea
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-01-23 Released: 2026-01-28 
• Deposition Author(s): Wu, B., Yu, L., Wang, Y.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.240 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of Aromatic Dioxygenases CpuAdo(Coniochaeta pulveracea)

Wu, B., Yu, L., Wang, Y.H.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 133.09 kDa 
• Atom Count: 9,494 
• Modeled Residue Count: 1,086 
• Deposited Residue Count: 1,170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lignostilbene dioxygenase	A, B	585	Coniochaeta pulveracea	Mutation(s): 0  Gene Names: DL546_006478
UniProt
Find proteins for A0A420Y5X8 (Coniochaeta pulveracea) Explore A0A420Y5X8  Go to UniProtKB:  A0A420Y5X8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE (Subject of Investigation/LOI)	C [auth A], E [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.240 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.902	α = 90
b = 90.052	β = 90
c = 194.065	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-28 
Deposition Author(s): Wu, B., Yu, L., Wang, Y.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32402025

Revision History  

• Version 1.0: 2026-01-28
  Type: Initial release