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- PDB-6ju4: Aspergillus oryzae pro-tyrosinase F513Y mutant -

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Basic information

Entry
Database: PDB / ID: 6ju4
TitleAspergillus oryzae pro-tyrosinase F513Y mutant
ComponentsTyrosinase
KeywordsOXIDOREDUCTASE / Tyrosinase / Copper enzyme / dinuclear copper center
Function / homology
Function and homology information


tyrosinase / tyrosinase activity / melanin biosynthetic process / nucleus / metal ion binding
Similarity search - Function
Domain of unknown function DUF1907 / DUF1907 / Tyosinase, C-terminal / Tyrosinase C-terminal domain / 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
Similarity search - Domain/homology
COPPER (II) ION / tyrosinase
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.35 Å
AuthorsFujieda, N. / Umakoshi, K. / Nishikawa, Y. / Kurisu, G. / Itoh, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyCREST(JPMJCR16P1) Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Copper-Oxygen Dynamics in the Tyrosinase Mechanism.
Authors: Fujieda, N. / Umakoshi, K. / Ochi, Y. / Nishikawa, Y. / Yanagisawa, S. / Kubo, M. / Kurisu, G. / Itoh, S.
History
DepositionApr 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_conn_type
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _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 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosinase
B: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,0156
Polymers142,7612
Non-polymers2544
Water14,952830
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-13 kcal/mol
Surface area38530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.220, 118.143, 79.347
Angle α, β, γ (deg.)90.00, 91.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosinase


Mass: 71380.578 Da / Num. of mol.: 2 / Mutation: F513Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: OAory_01107480 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S9DK56, tyrosinase
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 830 / Source method: isolated from a natural source / Formula: H2O

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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: 1.82 Å3/Da / Density % sol: 32.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 19% polyethylene glycol (PEG) 3350, 30mM NH4NO3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 216891 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 19.6
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 10767 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXL-97refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: AB INITIO
Starting model: 3W6W

3w6w


Resolution: 1.35→30 Å / Num. parameters: 82187 / Num. restraintsaints: 146176 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 10895 5 %RANDOM
Rwork0.1546 ---
obs0.157 216842 99.9 %-
Refine analyzeNum. disordered residues: 29 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 9525.3
Refinement stepCycle: LAST / Resolution: 1.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8694 0 58 844 9596
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0063
X-RAY DIFFRACTIONs_angle_d0.0196
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.3701
X-RAY DIFFRACTIONs_zero_chiral_vol0.0616
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.0616
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.0286
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.0452
X-RAY DIFFRACTIONs_approx_iso_adps0

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