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- PDB-5z0m: Crystal structure of copper-bound H63F-mutated tyrosinase from St... -

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Basic information

Entry
Database: PDB / ID: 5z0m
TitleCrystal structure of copper-bound H63F-mutated tyrosinase from Streptomyces castaneoglobisporus in complex with the caddie protein obtained by soaking in the hydroxylamine-containing solution for 12h at 298K
Components
  • MelC
  • Tyrosinase
KeywordsOXIDOREDUCTASE/METAL BINDING PROTEIN / tyrosinase / catalytic mechanism / OXIDOREDUCTASE-METAL BINDING PROTEIN 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: 1.7 Å
AuthorsMatoba, Y. / Sugiyama, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
KAKENHI25109530, 15H009470 Japan
CitationJournal: To Be Published
Title: Catalytic mechanism of tyrosinase implied from the quinone formation on the Tyr98 residue of the caddie protein
Authors: Matoba, Y. / Sugiyama, M.
History
DepositionDec 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.conn_type_id / _struct_conn.id / _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_conn_type.id
Revision 2.0Sep 17, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_src_gen / pdbx_entry_details / pdbx_struct_conn_angle / pdbx_struct_mod_residue / struct / struct_conn / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _entity.details / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_host_org_strain / _pdbx_entry_details.sequence_details / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct.title / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosinase
B: MelC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,76711
Polymers46,2042
Non-polymers5639
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-44 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.910, 97.350, 54.920
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-580-

HOH

21A-595-

HOH

31A-633-

HOH

41A-644-

HOH

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Components

#1: Protein Tyrosinase


Mass: 32098.592 Da / Num. of mol.: 1 / Mutation: H63F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces castaneoglobisporus (bacteria)
Strain: HUT6202 / Gene: tyrC / Plasmid: pET-mel2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q83WS2, tyrosinase
#2: Protein MelC / caddie protein


Mass: 14105.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TYR98 IN PROTEIN MELC WAS PARTIALLY HYDROXYLATED TO DAH.
Source: (gene. exp.) Streptomyces castaneoglobisporus (bacteria)
Strain: HUT6202 / Gene: orf378 / Plasmid: pET-mel2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q83WS1
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 1.93 Å3/Da / Density % sol: 34.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 3350, SODIUM NITRATE, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 35544 / % possible obs: 90.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 28.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3515 / % possible all: 91.8

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Processing

Software
NameClassification
SHELXL-97refinement
CNSphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→30 Å / Num. parameters: 28497 / Num. restraintsaints: 35410 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 1806 5.4 %RANDOM
all0.1432 33587 --
obs0.1422 33587 90.6 %-
Refine analyzeNum. disordered residues: 14 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3120.4
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 42 341 3163
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.026
X-RAY DIFFRACTIONs_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.045
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.012
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.002
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.027
X-RAY DIFFRACTIONs_approx_iso_adps0.075

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