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- PDB-6qxd: Crystal Structure of tyrosinase from Bacillus megaterium with JKB... -

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Basic information

Entry
Database: PDB / ID: 6qxd
TitleCrystal Structure of tyrosinase from Bacillus megaterium with JKB 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-JKB / Tyrosinase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.317 Å
AuthorsDeri Zenaty, B. / Gitto, R. / Pazy, Y. / Fishman, A.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation419/15 Israel
CitationJournal: Eur.J.Med.Chem. / Year: 2019
Title: Exploiting the 1-(4-fluorobenzyl)piperazine fragment for the development of novel tyrosinase inhibitors as anti-melanogenic agents: Design, synthesis, structural insights and biological profile.
Authors: Ielo, L. / Deri, B. / Germano, M.P. / Vittorio, S. / Mirabile, S. / Gitto, R. / Rapisarda, A. / Ronsisvalle, S. / Floris, S. / Pazy, Y. / Fais, A. / Fishman, A. / De Luca, L.
History
DepositionMar 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: Tyrosinase
B: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2217
Polymers66,5792
Non-polymers6435
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-40 kcal/mol
Surface area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.129, 78.263, 84.873
Angle α, β, γ (deg.)90.00, 105.82, 90.00
Int Tables number4
Space group name H-MP1211

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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 (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-JKB / (2,4-dinitrophenyl)-[4-[(4-fluorophenyl)methyl]piperazin-1-yl]methanone


Mass: 388.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17FN4O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 18% PEG 8000, 0.1M sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.317→46.021 Å / Num. obs: 26119 / % possible obs: 98.7 % / Redundancy: 4.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.052 / Rrim(I) all: 0.116 / Net I/σ(I): 8
Reflection shellResolution: 2.317→2.357 Å / Rmerge(I) obs: 0.754 / CC1/2: 0.856 / Rpim(I) all: 0.386 / Rrim(I) all: 0.85

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Processing

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

4p6r


Resolution: 2.317→46.021 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.19
RfactorNum. reflection% reflection
Rfree0.2481 1223 4.69 %
Rwork0.199 --
obs0.2011 26094 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.317→46.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 32 70 4810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034894
X-RAY DIFFRACTIONf_angle_d0.7666670
X-RAY DIFFRACTIONf_dihedral_angle_d13.7791791
X-RAY DIFFRACTIONf_chiral_restr0.03664
X-RAY DIFFRACTIONf_plane_restr0.004885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3171-2.40990.36661600.31212763X-RAY DIFFRACTION99
2.4099-2.51960.33741460.28612728X-RAY DIFFRACTION99
2.5196-2.65240.32991120.26422735X-RAY DIFFRACTION98
2.6524-2.81860.31471600.24592751X-RAY DIFFRACTION99
2.8186-3.03620.28691320.22562776X-RAY DIFFRACTION99
3.0362-3.34160.2511320.21722736X-RAY DIFFRACTION99
3.3416-3.8250.22681170.19692790X-RAY DIFFRACTION98
3.825-4.81820.22131230.16192814X-RAY DIFFRACTION99
4.8182-46.03040.20591410.17022778X-RAY DIFFRACTION98

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