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- PDB-4j6v: Crystal Structure of Tyrosinase from Bacillus megaterium N205D mutant -

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Basic information

Entry
Database: PDB / ID: 4j6v
TitleCrystal Structure of Tyrosinase from Bacillus megaterium N205D 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
COPPER (II) ION / Tyrosinase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)70,6384
Polymers70,5112
Non-polymers1272
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.900, 78.330, 82.160
Angle α, β, γ (deg.)90.000, 105.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosinase


Mass: 35255.461 Da / Num. of mol.: 2 / Mutation: N205D
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: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
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: ID23-1 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→79.172 Å / Num. all: 51526 / Num. obs: 51526 / % possible obs: 97.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-23.50.2511.62659675310.25198.1
2-2.123.60.1282.42592771440.12898.4
2.12-2.273.50.1233.82363567420.12398.6
2.27-2.453.60.0768.12255362980.07698.9
2.45-2.693.60.067.62100158010.0699.2
2.69-33.60.05211.81884052720.05299.3
3-3.473.50.05311.21643746630.05399.3
3.47-4.253.30.05411.21279939380.05498.7
4.25-6.0130.05410.6858929050.05494.3
6.01-43.8413.10.0639377512320.06371.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.84 Å
Translation2.5 Å43.84 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASER2.3.0phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→39.392 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.8608 / SU ML: 0.19 / σ(F): 1.36 / Phase error: 21.28 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2101 2618 5.08 %
Rwork0.1931 --
obs0.194 51493 97.33 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.78 Å2 / ksol: 0.392 e/Å3
Displacement parametersBiso max: 114.38 Å2 / Biso mean: 25.0159 Å2 / Biso min: 6.56 Å2
Baniso -1Baniso -2Baniso -3
1-5.9169 Å20 Å2-5.7336 Å2
2---4.267 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4700 0 2 335 5037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194860
X-RAY DIFFRACTIONf_angle_d1.3966624
X-RAY DIFFRACTIONf_chiral_restr0.109660
X-RAY DIFFRACTIONf_plane_restr0.012878
X-RAY DIFFRACTIONf_dihedral_angle_d16.3281774
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.93460.33731420.27532535267798
1.9346-1.97180.24391330.2312584271798
1.9718-2.0120.21641330.21642583271698
2.012-2.05580.24781610.20642569273098
2.0558-2.10360.21811290.20992613274298
2.1036-2.15620.25541370.20922569270698
2.1562-2.21450.2281380.21172596273499
2.2145-2.27960.26751130.22352633274699
2.2796-2.35320.25391470.20872551269899
2.3532-2.43730.18671540.19382592274699
2.4373-2.53490.21621240.19322632275699
2.5349-2.65020.22661550.19072618277399
2.6502-2.78990.20431250.19312620274599
2.7899-2.96460.21981370.19772628276599
2.9646-3.19340.19581450.18912625277099
3.1934-3.51460.18371410.18312610275199
3.5146-4.02280.18081330.16852629276299
4.0228-5.06660.17621360.15872549268595
5.0666-39.40040.19861350.19512139227479

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