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), 0.165 (DCC)
R-Value Work:
0.131 (Depositor), 0.129 (DCC)
R-Value Observed:
0.132 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

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

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q83WS2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q83WS1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth A], J [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] K [auth B] 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		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B]
PER Query on PER Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PEROXIDE ION O₂ ANAIPYUSIMHBEL-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free: 0.170 (Depositor), 0.165 (DCC)
R-Value Work: 0.131 (Depositor), 0.129 (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

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View more in-depth experimental data

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 (Full details and data files)

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

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

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2