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- PDB-9h2o: Crystal structure of apo-tyrosinase from Priestia megaterium -

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Basic information

Entry
Database: PDB / ID: 9h2o
TitleCrystal structure of apo-tyrosinase from Priestia megaterium
ComponentsTyrosinase
KeywordsMETAL BINDING PROTEIN / Tyrosinase / Monophenolase / Diphenolase / Type-3 Copper
Function / homologyTyrosinase 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 / oxidoreductase activity / metal ion binding / Tyrosinase
Function and homology information
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsEnglund, A.N.B. / Rohr, A.K.
Funding support Norway, 1items
OrganizationGrant numberCountry
Norwegian Research Council301022 Norway
CitationJournal: To Be Published
Title: An Alternative Reaction Mechanism of C-H Bond Activation in Tyrosinase
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


Theoretical massNumber of molelcules
Total (without water)70,5132
Polymers70,5132
Non-polymers00
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-8 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.648, 78.223, 85.526
Angle α, β, γ (deg.)90.000, 104.934, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Tyrosinase


Mass: 35256.418 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.68 %
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: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.8→46.05 Å / Num. obs: 54965 / % possible obs: 97.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 23.86 Å2 / CC1/2: 0.987 / Net I/σ(I): 6.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.8 % / Num. unique obs: 5206 / CC1/2: 0.614 / R split: 1.1 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHENIX1.19_4092phasing
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→41.32 Å / SU ML: 0.2801 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.5282
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2575 2582 4.7 %
Rwork0.1827 52371 -
obs0.1863 54953 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.77 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4689 0 0 331 5020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00744856
X-RAY DIFFRACTIONf_angle_d1.06526619
X-RAY DIFFRACTIONf_chiral_restr0.0586663
X-RAY DIFFRACTIONf_plane_restr0.0099881
X-RAY DIFFRACTIONf_dihedral_angle_d6.269631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.39081300.2912610X-RAY DIFFRACTION88.02
1.83-1.870.34521530.25672909X-RAY DIFFRACTION98.65
1.87-1.910.31021360.23692958X-RAY DIFFRACTION98.72
1.91-1.960.31341300.21732918X-RAY DIFFRACTION99.19
1.96-2.010.31551370.21922953X-RAY DIFFRACTION99.23
2.01-2.060.30821750.2132924X-RAY DIFFRACTION99.07
2.06-2.120.29721450.20542954X-RAY DIFFRACTION99.3
2.12-2.190.31391360.19312934X-RAY DIFFRACTION99.32
2.19-2.270.27931230.17912974X-RAY DIFFRACTION99.2
2.27-2.360.2821450.16592949X-RAY DIFFRACTION99.23
2.36-2.470.25231600.16812942X-RAY DIFFRACTION99.04
2.47-2.60.2361350.17222944X-RAY DIFFRACTION99.13
2.6-2.760.24871470.18392945X-RAY DIFFRACTION98.75
2.76-2.970.28981530.19132911X-RAY DIFFRACTION97.42
2.97-3.270.25261350.18412870X-RAY DIFFRACTION96.38
3.27-3.740.23791430.17442861X-RAY DIFFRACTION95.73
3.74-4.720.21641450.15242875X-RAY DIFFRACTION95.78
4.72-41.320.21471540.1732940X-RAY DIFFRACTION96.51

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