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- PDB-9h2n: Crystal structure of tyrosinase from Priestia megaterium F227Y mu... -

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Basic information

Entry
Database: PDB / ID: 9h2n
TitleCrystal structure of tyrosinase from Priestia megaterium F227Y mutant soaked in Cu(II) and sodium dithionite
ComponentsTyrosinase
KeywordsMETAL BINDING PROTEIN / Tyrosinase / Monophenolase / Diphenolase / Type-3 Copper / mutant
Function / homology
Function and homology information


oxidoreductase activity / metal ion binding
Similarity search - Function
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 speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEnglund, A.N.B. / Rohr, A.K.
Funding support Norway, 1items
OrganizationGrant numberCountry
Norwegian Research Council301022 Norway
CitationJournal: To be published
Title: A novel copper-tyrosyl site among type-3 copper proteins
Authors: Englund, A.N.B. / Rohr, A.K. / Dalleywater, E.L.
History
DepositionOct 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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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)70,8556
Polymers70,6012
Non-polymers2544
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-14 kcal/mol
Surface area22810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.514, 78.039, 150.075
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Tyrosinase


Mass: 35300.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: B2ZB02
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.97 Å3/Da / Density % sol: 37.58 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 0.1 M magnesium formate dihydrate, 15% PEG 3500

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2→75.04 Å / Num. obs: 38439 / % possible obs: 99.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 35.06 Å2 / CC1/2: 0.997 / Net I/σ(I): 5.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3741 / CC1/2: 0.71 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.19_4092phasing
PHENIX1.19_4092refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→75.04 Å / SU ML: 0.2795 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.8744
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.285 1994 5.2 %
Rwork0.2193 36320 -
obs0.2228 38314 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.68 Å2
Refinement stepCycle: LAST / Resolution: 2→75.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4684 0 4 145 4833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074851
X-RAY DIFFRACTIONf_angle_d0.9126614
X-RAY DIFFRACTIONf_chiral_restr0.0522663
X-RAY DIFFRACTIONf_plane_restr0.0097879
X-RAY DIFFRACTIONf_dihedral_angle_d5.9732633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.47321370.41032500X-RAY DIFFRACTION97.59
2.05-2.110.42541400.3832548X-RAY DIFFRACTION99.19
2.11-2.170.3881420.35222579X-RAY DIFFRACTION99.27
2.17-2.240.37531380.31482532X-RAY DIFFRACTION99.26
2.24-2.320.39351400.29312548X-RAY DIFFRACTION99.33
2.32-2.410.34291410.26252582X-RAY DIFFRACTION99.49
2.41-2.520.27191430.24822587X-RAY DIFFRACTION99.6
2.52-2.650.30361420.23792563X-RAY DIFFRACTION99.45
2.65-2.820.28241410.23622597X-RAY DIFFRACTION99.31
2.82-3.040.30621430.23612598X-RAY DIFFRACTION99.71
3.04-3.340.33231430.23052610X-RAY DIFFRACTION99.85
3.34-3.830.28831450.20442633X-RAY DIFFRACTION99.78
3.83-4.820.24521460.16262676X-RAY DIFFRACTION99.44
4.82-75.040.20941530.16452767X-RAY DIFFRACTION98.68

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