2ZWF | pdb_00002zwf

Crystal structure of the copper-bound tyrosinase in complex with a caddie protein from streptomyces castaneoglobisporus obtained by soaking the deoxy-form crystal in dioxygen-saturated solution for 80 minutes

PDB DOI: https://doi.org/10.2210/pdb2ZWF/pdb

Classification: OXIDOREDUCTASE/METAL TRANSPORT
Organism(s): Streptomyces castaneoglobisporus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-12-03 Released: 2009-12-15
Deposition Author(s): Matoba, Y., Sugiyama, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.212 (Depositor), 0.200 (DCC)
R-Value Work:
0.173 (Depositor), 0.164 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Crystallographic evidence of drastic movement of a copper ion toward the substrate tyrosine for starting hydroxylation reaction of tyrosinase

Matoba, Y., Yoshitsu, H., Jeon, H.J., Oda, K., Noda, M., Kumagai, T., Sugiyama, M.

To be published.

Macromolecule Content

Total Structure Weight: 46.87 kDa
Atom Count: 3,258
Modeled Residue Count: 348
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 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

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MelC	B	134	Streptomyces castaneoglobisporus	Mutation(s): 0
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU 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 A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	C [auth A], D [auth A], E [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 E [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [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 G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B]	F [auth A], G [auth A], H [auth A], I [auth A], K [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] 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]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAH Query on DAH	B	L-PEPTIDE LINKING	C₉ H₁₁ N O₄		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.212 (Depositor), 0.200 (DCC)
R-Value Work: 0.173 (Depositor), 0.164 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.16	α = 90
b = 97.68	β = 90
c = 54.99	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-12-15

Deposition Author(s):

Matoba, Y.

Sugiyama, M.

Revision History (Full details and data files)

Version 1.0: 2009-12-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-08-31
Changes: Non-polymer description
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-30
Changes: Structure summary
Version 2.0: 2025-09-17
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary