5Z0E | pdb_00005z0e

Crystal structure of copper-bound tyrosinase from Streptomyces castaneoglobisporus in complex with the Y98F mutant of the caddie protein obtained by soaking in the hydroxylamine-containing solution for 2 h at 298 K

• PDB DOI: https://doi.org/10.2210/pdb5Z0E/pdb

• Classification: OXIDOREDUCTASE/METAL BINDING PROTEIN
• Organism(s): Streptomyces castaneoglobisporus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-12-19 Released: 2018-12-26 
• Deposition Author(s): Matoba, Y., Sugiyama, M.
• Funding Organization(s): KAKENHI

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free: 
  0.170 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.131 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.132 (Depositor) 

Starting Model: experimental

Literature

Catalytic mechanism of tyrosinase implied from the quinone formation on the Tyr98 residue of the caddie protein

Matoba, Y., Sugiyama, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 46.76 kDa 
• Atom Count: 3,264 
• Modeled Residue Count: 346 
• Deposited Residue Count: 415 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosinase	A	281	Streptomyces castaneoglobisporus	Mutation(s): 0  Gene Names: tyrC EC: 1.14.18.1
UniProt
Find proteins for Q83WS2 (Streptomyces castaneoglobisporus) Explore Q83WS2  Go to UniProtKB:  Q83WS2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MelC	B	134	Streptomyces castaneoglobisporus	Mutation(s): 1  Gene Names: orf378
UniProt
Find proteins for Q83WS1 (Streptomyces castaneoglobisporus) Explore Q83WS1  Go to UniProtKB:  Q83WS1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	C [auth A], D [auth A], J [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
NO3	F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
PER	E [auth A]	PEROXIDE ION O2 ANAIPYUSIMHBEL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free:  0.170 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.131 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.132 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.63	α = 90
b = 96.93	β = 90
c = 54.51	γ = 90

Software Package:

Software Name	Purpose
CNS	phasing
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-26 
Deposition Author(s): Matoba, Y., Sugiyama, M.

---

Funding Organization	Location	Grant Number
KAKENHI	Japan	25109530, 15H009470

Revision History  

• Version 1.0: 2018-12-26
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description