9KOL | pdb_00009kol

Crystal structure of a Ruthenium and Copper-substituted small laccase

• PDB DOI: https://doi.org/10.2210/pdb9KOL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces coelicolor A3(2)
• Expression System: Escherichia coli #1/H766
• Mutation(s): No 


• Deposited: 2024-11-20 Released: 2025-10-01 
• Deposition Author(s): Yang, X., Fan, S., Liu, J., Wu, W., Chen, X., Ji, W., Li, S., Xue, Y., Sun, X., Wang, M., Wu, F., Yu, P., Mao, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.188 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Remolding laccase for whole-cell and in vivo modulation of dopamine signal

Yang, X., Fan, S., Liu, J., Wu, W., Chen, X., Ji, W., Li, S., Xue, Y., Sun, X., Wang, M., Wu, F., Yu, P., Mao, L.

(2025) Sci Adv 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30.84 kDa 
• Atom Count: 2,435 
• Modeled Residue Count: 279 
• Deposited Residue Count: 279 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper oxidase	A	279	Streptomyces coelicolor A3(2)	Mutation(s): 0  Gene Names: SCO6712, SC4C6.22
UniProt
Find proteins for Q9XAL8 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9XAL8  Go to UniProtKB:  Q9XAL8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RU (Subject of Investigation/LOI)	D [auth A]	RUTHENIUM ION Ru BPEVHDGLPIIAGH-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)	B [auth A], C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.188 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.441	α = 90
b = 177.441	β = 90
c = 177.441	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Yang, X., Fan, S., Liu, J., Wu, W., Chen, X., Ji, W., Li, S., Xue, Y., Sun, X., Wang, M., Wu, F., Yu, P., Mao, L.

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

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release