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- PDB-6j2u: Crystal structure of Tyrosinase caddy protein(MelC1)with Tyrosina... -

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Basic information

Entry
Database: PDB / ID: 6j2u
TitleCrystal structure of Tyrosinase caddy protein(MelC1)with Tyrosinase (MelC2)from Streptomyces avermitilis in complex with Zinc ion
Components
  • Tyrosinase
  • Tyrosinase co-factor protein
KeywordsOXIDOREDUCTASE / Citrate synthase / Metallosphaera sedula
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
Tyrosinase co-factor protein / Tyrosinase
Similarity search - Component
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsLee, S.-H. / Hong, H. / Kim, K.-J.
CitationJournal: To Be Published
Title: Crystal structure of Tyrosinase caddy protein(MelC1)with tyrosinase (MelC2)from Streptomyces avermitilis in complex with Zinc ion
Authors: Lee, S.-H. / Hong, H. / Kim, K.-J.
History
DepositionJan 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
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_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_seq_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_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosinase co-factor protein
B: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4924
Polymers44,3612
Non-polymers1312
Water9,314517
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-95 kcal/mol
Surface area13370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.998, 71.828, 48.524
Angle α, β, γ (deg.)90.000, 113.720, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tyrosinase co-factor protein


Mass: 12111.513 Da / Num. of mol.: 1 / Fragment: MelC1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Gene: melC1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q93HL1
#2: Protein Tyrosinase


Mass: 32249.723 Da / Num. of mol.: 1 / Fragment: MelC2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Gene: melC2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q93HL2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 20% polyethylene glycol 3350 and 0.2 M Lithium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.3→60.12 Å / Num. obs: 91179 / % possible obs: 98.4 % / Redundancy: 3.5 % / CC1/2: 0.993 / Net I/σ(I): 29.3
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 4459 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z0D

5z0d


Resolution: 1.3→60.12 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1721 4596 -
Rwork0.1549 --
obs0.981485 91179 98.4 %
Displacement parametersBiso max: 59.83 Å2 / Biso min: 2.31 Å2
Refinement stepCycle: final / Resolution: 1.3→60.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 2 520 3247
Biso mean--20.76 26.33 -
Num. residues----345
LS refinement shellResolution: 1.3→1.32 Å
RfactorNum. reflection% reflection
Rfree0.155 --
Rwork0.172 --
obs-4459 96.7 %

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