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- PDB-5oae: Crystal Structure of tyrosinase from Bacillus megaterium with SVF... -

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Basic information

Entry
Database: PDB / ID: 5oae
TitleCrystal Structure of tyrosinase from Bacillus megaterium with SVF inhibitor in the active site
ComponentsTyrosinase
KeywordsOXIDOREDUCTASE / Tyrosinase Inhibitor Ligand
Function / homology
Function and homology information


tyrosinase activity / melanin biosynthetic process / pigmentation / metal ion binding
Similarity search - Function
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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / Chem-SVF / Tyrosinase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDeri, B. / Gitto, R. / Pazy Benhar, Y. / Fishman, A.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation419/15 Israel
CitationJournal: J. Med. Chem. / Year: 2018
Title: Targeting Tyrosinase: Development and Structural Insights of Novel Inhibitors Bearing Arylpiperidine and Arylpiperazine Fragments.
Authors: Ferro, S. / Deri, B. / Germano, M.P. / Gitto, R. / Ielo, L. / Buemi, M.R. / Certo, G. / Vittorio, S. / Rapisarda, A. / Pazy, Y. / Fishman, A. / De Luca, L.
History
DepositionJun 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: Tyrosinase
B: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3038
Polymers66,5792
Non-polymers7256
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-13 kcal/mol
Surface area23200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.450, 84.100, 89.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tyrosinase


Mass: 33289.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2ZB02
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-SVF / 1-[4-[(4-fluorophenyl)methyl]piperidin-1-yl]ethanone


Mass: 235.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18FNO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 44.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 8000, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.7→39.59 Å / Num. obs: 15340 / % possible obs: 92 % / Redundancy: 3.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.06 / Net I/σ(I): 10.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2286 / CC1/2: 0.52 / Rpim(I) all: 0.378 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P6R

4p6r


Resolution: 2.7→38.956 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.54
RfactorNum. reflection% reflection
Rfree0.2609 770 5.03 %
Rwork0.2164 --
obs0.2185 15313 90.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→38.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4699 0 38 44 4781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034891
X-RAY DIFFRACTIONf_angle_d0.7316665
X-RAY DIFFRACTIONf_dihedral_angle_d12.7411785
X-RAY DIFFRACTIONf_chiral_restr0.03665
X-RAY DIFFRACTIONf_plane_restr0.004883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.86910.39451550.34812446X-RAY DIFFRACTION95
2.8691-3.09060.3481350.29542453X-RAY DIFFRACTION94
3.0906-3.40140.27891370.25622417X-RAY DIFFRACTION91
3.4014-3.89320.22781260.20442423X-RAY DIFFRACTION92
3.8932-4.90350.19781200.17662386X-RAY DIFFRACTION89
4.9035-38.95980.2511970.18312418X-RAY DIFFRACTION85

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