2ZMZ | pdb_00002zmz

The 1.37-A crystal structure of the hydroxylamine-induced deoxy-form of the copper-bound tyrosinase in complex with a caddie protein from Streptomyces castaneoglobisporus

• PDB DOI: https://doi.org/10.2210/pdb2ZMZ/pdb

• Classification: OXIDOREDUCTASE/METAL TRANSPORT
• Organism(s): Streptomyces castaneoglobisporus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-04-21 Released: 2009-05-05 
• Deposition Author(s): Matoba, Y., Sugiyama, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 
  0.232 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

X-Ray Snapshots of a Hydroxylation Mechanism of Tyrosinase

Matoba, Y., Yoshitsu, H., Jeon, H.-J., Oda, K., Noda, M., Kumagai, T., 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: 46.86 kDa 
• Atom Count: 3,295 
• Modeled Residue Count: 352 
• 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
CADDIE	B	134	Streptomyces castaneoglobisporus	Mutation(s): 0  Gene Names: ORF378
UniProt
Find proteins for Q83WS1 (Streptomyces castaneoglobisporus) Explore Q83WS1  Go to UniProtKB:  Q83WS1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU1	C [auth A], D [auth A], I [auth B]	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N
NO3	E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free:  0.232 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.18	α = 90
b = 98.03	β = 90
c = 55.2	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-05 
Deposition Author(s): Matoba, Y., Sugiyama, M.

Revision History  

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description