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- PDB-4j6u: Crystal Structure of Tyrosinase from Bacillus megaterium N205A mutant -

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Basic information

Entry
Database: PDB / ID: 4j6u
TitleCrystal Structure of Tyrosinase from Bacillus megaterium N205A mutant
ComponentsTyrosinase
KeywordsOXIDOREDUCTASE / type 3 copper proteins
Function / homology
Function and homology information


oxidoreductase activity / 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
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsKanteev, M. / Goldfeder, M. / Adir, N. / Fishman, A.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 2013
Title: The mechanism of copper uptake by tyrosinase from Bacillus megaterium.
Authors: Kanteev, M. / Goldfeder, M. / Chojnacki, M. / Adir, N. / Fishman, A.
#1: Journal: J.Mol.Biol. / Year: 2011
Title: First structures of an active bacterial tyrosinase reveal copper plasticity.
Authors: Sendovski, M. / Kanteev, M. / Ben-Yosef, V.S. / Adir, N. / Fishman, A.
History
DepositionFeb 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)70,4232
Polymers70,4232
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.080, 78.770, 85.990
Angle α, β, γ (deg.)90.000, 104.630, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosinase


Mass: 35211.453 Da / Num. of mol.: 2 / Mutation: N205A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2ZB02, tyrosinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate, pH 6.5, 18% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.385→83.202 Å / Num. all: 24549 / Num. obs: 24549 / % possible obs: 98.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.385-2.513.20.1913.31115435260.19198
2.51-2.673.50.1653.61192634010.16599.5
2.67-2.853.50.1423.91118632010.14299.5
2.85-3.083.50.1125.61040029610.11299.6
3.08-3.373.50.1016954727330.10199.4
3.37-3.773.40.1184.7831924820.11899.2
3.77-4.353.40.0837.5755022160.08399.4
4.35-5.333.40.0788628918560.07899.5
5.33-7.543.10.0817.2444414370.08199.4
7.54-28.6013.40.0511.825137360.0589

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 37.68 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.6 Å
Translation2.5 Å28.6 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NM8

3nm8


Resolution: 2.5→28.601 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8025 / SU ML: 0.27 / σ(F): 1.37 / Phase error: 26.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2407 1070 5.01 %
Rwork0.2075 --
obs0.2092 21358 98.87 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.563 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso max: 101.06 Å2 / Biso mean: 38.6591 Å2 / Biso min: 11.76 Å2
Baniso -1Baniso -2Baniso -3
1-4.4163 Å20 Å220.9707 Å2
2---19.0628 Å20 Å2
3---14.6465 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4677 0 0 101 4778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0234833
X-RAY DIFFRACTIONf_angle_d1.5556586
X-RAY DIFFRACTIONf_chiral_restr0.108659
X-RAY DIFFRACTIONf_plane_restr0.011874
X-RAY DIFFRACTIONf_dihedral_angle_d16.7281766
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.61370.27041200.23882520264099
2.6137-2.75140.28041400.24582520266099
2.7514-2.92360.29731300.22972555268599
2.9236-3.14910.29041290.2252546267599
3.1491-3.46550.23441200.22662551267199
3.4655-3.96590.26991470.21542532267999
3.9659-4.99220.17671430.16592540268399
4.9922-28.60260.21331410.18732524266596

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