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- PDB-2zwe: Crystal structure of the copper-bound tyrosinase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 2zwe
TitleCrystal 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 40 minutes
Components
  • MelC
  • Tyrosinase
KeywordsOXIDOREDUCTASE/METAL TRANSPORT / TYROSINASE / BINARY COMPLEX / TYPE-3 COPPER / DIOXYGEN / COPPER TRANSFER / OXIDOREDUCTASE-METAL TRANSPORT COMPLEX
Function / homology
Function and homology information


melanin biosynthetic process / oxidoreductase activity / copper ion binding / metal ion binding
Similarity search - Function
Tyrosinase co-factor MelC1 / Tyrosinase co-factor MelC1 / protein ne1242 fold / protein ne1242 domain like / Copper chaperone GriE/MELC1 superfamily / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Tyrosinase CuA-binding region signature. / : / Common central domain of tyrosinase ...Tyrosinase co-factor MelC1 / Tyrosinase co-factor MelC1 / protein ne1242 fold / protein ne1242 domain like / Copper chaperone GriE/MELC1 superfamily / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Tyrosinase CuA-binding region signature. / : / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / NITRATE ION / MelC / Tyrosinase
Similarity search - Component
Biological speciesStreptomyces castaneoglobisporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsMatoba, Y. / Sugiyama, M.
Citation
Journal: To be Published
Title: Crystallographic evidence of drastic movement of a copper ion toward the substrate tyrosine for starting hydroxylation reaction of tyrosinase
Authors: Matoba, Y. / Yoshitsu, H. / Jeon, H.J. / Oda, K. / Noda, M. / Kumagai, T. / Sugiyama, M.
#1: Journal: J.Biol.Chem. / Year: 2006
Title: Crystallographic evidence that the dinuclear copper center of tyrosinase is flexible during catalysis
Authors: Matoba, Y. / Kumagai, T. / Yamamoto, A. / Yoshitsu, H. / Sugiyama, M.
History
DepositionDec 3, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 31, 2011Group: Non-polymer description
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 2.0Sep 17, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / entity_name_com / entity_poly / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_struct_conn_angle / pdbx_struct_mod_residue / struct_conn / struct_ref / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_entry_details.sequence_details / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_mod_residue.details / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_ref.db_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosinase
B: MelC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,81210
Polymers46,3092
Non-polymers5028
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-52 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.240, 97.880, 55.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-504-

CU

21A-938-

HOH

31A-939-

HOH

41A-941-

HOH

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Components

#1: Protein Tyrosinase


Mass: 32089.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces castaneoglobisporus (bacteria)
Strain: HUT 6202 / Plasmid: PET-MEL2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q83WS2, tyrosinase
#2: Protein MelC / CADDIE PROTEIN ORF378


Mass: 14219.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces castaneoglobisporus (bacteria)
Strain: HUT 6202 / Plasmid: PET-MEL2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q83WS1
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 35.25 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 3350, SODIUM NITRATE, HEPES, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.8 / Wavelength: 0.8 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.32→100 Å / Num. all: 82482 / Num. obs: 82482 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 30.9
Reflection shellResolution: 1.32→1.37 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 3.2 / Num. unique all: 8236 / Rsym value: 0.303 / % possible all: 99.8

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Processing

Software
NameClassification
CNSrefinement
SHELXL-97refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WX3

1wx3
PDB Unreleased entry


Resolution: 1.32→30 Å / Num. parameters: 13335 / Num. restraintsaints: 12024 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 4047 5.3 %RANDOM
Rwork0.1745 ---
all0.1746 80432 --
obs0.1746 80432 96.5 %-
Refine analyzeNum. disordered residues: 11 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3273.79
Refinement stepCycle: LAST / Resolution: 1.32→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 20 437 3279
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.068
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.035
X-RAY DIFFRACTIONs_approx_iso_adps0

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