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- PDB-9h29: Crystal structure of tyrosinase from Priestia megaterium F227Y mu... -

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Basic information

Entry
Database: PDB / ID: 9h29
TitleCrystal structure of tyrosinase from Priestia megaterium F227Y mutant soaked in Cu(II)
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: 2.17 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 11, 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)70,9828
Polymers70,6012
Non-polymers3816
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-60 kcal/mol
Surface area22720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.423, 78.903, 83.054
Angle α, β, γ (deg.)90.000, 106.050, 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: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
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: 2.17→79.82 Å / Num. obs: 34552 / % possible obs: 95.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 31.03 Å2 / CC1/2: 0.989 / Net I/σ(I): 8.8
Reflection shellResolution: 2.17→2.2 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3393 / CC1/2: 0.829 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX1.19_4092phasing
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→39.91 Å / SU ML: 0.3006 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7517
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2577 1661 4.81 %
Rwork0.2024 32878 -
obs0.2052 34539 95.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.53 Å2
Refinement stepCycle: LAST / Resolution: 2.17→39.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4711 0 6 256 4973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814879
X-RAY DIFFRACTIONf_angle_d0.96556649
X-RAY DIFFRACTIONf_chiral_restr0.0548663
X-RAY DIFFRACTIONf_plane_restr0.0097884
X-RAY DIFFRACTIONf_dihedral_angle_d6.0308636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.230.29721080.23492709X-RAY DIFFRACTION94.47
2.23-2.30.29831140.22742687X-RAY DIFFRACTION94.06
2.3-2.380.30511460.21462694X-RAY DIFFRACTION94.07
2.38-2.480.27461520.22012679X-RAY DIFFRACTION94.3
2.48-2.590.28431520.22332698X-RAY DIFFRACTION94.87
2.59-2.730.33481170.22682730X-RAY DIFFRACTION95.44
2.73-2.90.32391440.23172767X-RAY DIFFRACTION97.88
2.9-3.120.33151550.23052782X-RAY DIFFRACTION98.49
3.12-3.440.28171410.22192832X-RAY DIFFRACTION97.51
3.44-3.930.22611320.1892571X-RAY DIFFRACTION89.92
3.93-4.950.20561510.16362843X-RAY DIFFRACTION98.75
4.96-39.910.20251490.17942886X-RAY DIFFRACTION98.73

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