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- PDB-9h1t: Crystal structure of apo-tyrosinase from Priestia megaterium F227... -

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Basic information

Entry
Database: PDB / ID: 9h1t
TitleCrystal structure of apo-tyrosinase from Priestia megaterium F227Y mutant
ComponentsTyrosinase
KeywordsMETAL BINDING PROTEIN / Tyrosinase / Monophenolase / Diphenolase / Type-3 Copper / mutant
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: 2.14 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 10, 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)70,6012
Polymers70,6012
Non-polymers00
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-7 kcal/mol
Surface area22190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.894, 78.631, 86.587
Angle α, β, γ (deg.)90.000, 103.973, 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: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
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: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.14→57.43 Å / Num. obs: 33209 / % possible obs: 96.69 % / Redundancy: 1.9 % / CC1/2: 0.825 / Net I/σ(I): 7.6
Reflection shellResolution: 2.14→2.22 Å / Redundancy: 2 % / Mean I/σ(I) obs: 4.3 / Num. unique obs: 3342 / CC1/2: 0.804 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.19_4092phasing
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→40.01 Å / SU ML: 0.2661 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1687
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2826 1702 5.13 %
Rwork0.2038 31496 -
obs0.2079 33198 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.43 Å2
Refinement stepCycle: LAST / Resolution: 2.14→40.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4656 0 0 323 4979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734821
X-RAY DIFFRACTIONf_angle_d0.95496572
X-RAY DIFFRACTIONf_chiral_restr0.0512660
X-RAY DIFFRACTIONf_plane_restr0.0096873
X-RAY DIFFRACTIONf_dihedral_angle_d5.8034627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.210.29091470.20742635X-RAY DIFFRACTION97.31
2.21-2.280.2631500.20022657X-RAY DIFFRACTION98.08
2.28-2.360.30631190.20382658X-RAY DIFFRACTION97.85
2.36-2.450.31911440.20632633X-RAY DIFFRACTION98.3
2.45-2.560.28461430.21162674X-RAY DIFFRACTION97.85
2.56-2.70.28571390.20612654X-RAY DIFFRACTION98.41
2.7-2.870.27161450.2052640X-RAY DIFFRACTION97.58
2.87-3.090.25081500.20862575X-RAY DIFFRACTION95.28
3.09-3.40.32941410.21772451X-RAY DIFFRACTION89.91
3.4-3.890.25371400.18872630X-RAY DIFFRACTION96.99
3.89-4.90.23661180.17552674X-RAY DIFFRACTION96.74
4.9-40.010.20541660.18032615X-RAY DIFFRACTION94.75

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