9H2N | pdb_00009h2n

Crystal structure of tyrosinase from Priestia megaterium F227Y mutant soaked in Cu(II) and sodium dithionite

PDB DOI: https://doi.org/10.2210/pdb9H2N/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Priestia megaterium
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-10-14 Released: 2025-10-29
Deposition Author(s): Englund, A.N.B., Rohr, A.K.
Funding Organization(s): Norwegian Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.285 (Depositor), 0.285 (DCC)
R-Value Work:
0.219 (Depositor), 0.221 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

A novel copper-tyrosyl site among type-3 copper proteins

Englund, A.N.B., Rohr, A.K., Dalleywater, E.L.

To be published.

Macromolecule Content

Total Structure Weight: 70.86 kDa
Atom Count: 4,844
Modeled Residue Count: 573
Deposited Residue Count: 606
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosinase	A, B	303	Priestia megaterium	Mutation(s): 1
UniProt
Find proteins for B2ZB02 (Priestia megaterium) Explore B2ZB02 Go to UniProtKB: B2ZB02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2ZB02
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	C [auth A], D [auth A], E [auth B], F [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.285 (Depositor), 0.285 (DCC)
R-Value Work: 0.219 (Depositor), 0.221 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.514	α = 90
b = 78.039	β = 90
c = 150.075	γ = 90

Software Package:

Software Name	Purpose
PHENIX	phasing
PHENIX	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-29

Deposition Author(s):

Englund, A.N.B.

Funding Organization	Location	Grant Number
Norwegian Research Council	Norway	301022

Revision History (Full details and data files)

Version 1.0: 2025-10-29
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.