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- PDB-4p6r: Crystal Structure of tyrosinase from Bacillus megaterium with tyr... -

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Basic information

Entry
Database: PDB / ID: 4p6r
TitleCrystal Structure of tyrosinase from Bacillus megaterium with tyrosine in the active site
ComponentsTyrosinase
KeywordsOXIDOREDUCTASE / tyrosine / type 3 copper proteins
Function / homology
Function and homology information


tyrosinase activity / melanin biosynthetic process / pigmentation / 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
TYROSINE / Tyrosinase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsGoldfeder, M. / Kanteev, M. / Adir, N. / Fishman, A.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation193/11 Israel
CitationJournal: Nat Commun / Year: 2014
Title: Determination of tyrosinase substrate-binding modes reveals mechanistic differences between type-3 copper proteins.
Authors: Goldfeder, M. / Kanteev, M. / Isaschar-Ovdat, S. / Adir, N. / Fishman, A.
History
DepositionMar 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
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.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.value / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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

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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)67,2038
Polymers66,5792
Non-polymers6246
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.800, 78.680, 85.820
Angle α, β, γ (deg.)90.000, 102.630, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosinase


Mass: 33289.266 Da / Num. of mol.: 2 / Fragment: UNP residues 4-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Plasmid: pET9d / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B2ZB02, tyrosinase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG8000, sodium cacodylate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→83.743 Å / Num. all: 31929 / Num. obs: 31929 / % possible obs: 97.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 19.17 Å2 / Rpim(I) all: 0.044 / Rrim(I) all: 0.083 / Rsym value: 0.07 / Net I/av σ(I): 7.297 / Net I/σ(I): 11.2 / Num. measured all: 108133
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.323.30.1534.11512645750.0970.1535.895.7
2.32-2.463.30.1125.81438543140.0710.1126.795.3
2.46-2.633.30.0996.71343240430.0640.0997.695.4
2.63-2.843.30.0857.41261838300.0540.0859.296.9
2.84-3.113.30.0738.41198136140.0470.07311.398.6
3.11-3.483.50.0669.21135732650.0410.06614.199.8
3.48-4.023.40.0629.41001929300.0390.06217.299.6
4.02-4.923.10.0579.4739223650.0360.05717.695.3
4.92-6.9640.05810772719340.0330.05818.8100
6.96-41.8723.90.0511.7409610590.0280.0519.397.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASERphasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.7.3_928)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→41.872 Å / FOM work R set: 0.7993 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2406 1620 5.08 %
Rwork0.1914 30278 -
obs0.194 31898 96.82 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.923 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 119.93 Å2 / Biso mean: 27.71 Å2 / Biso min: 6.69 Å2
Baniso -1Baniso -2Baniso -3
1-15.983 Å2-0 Å29.706 Å2
2---10.892 Å20 Å2
3----5.091 Å2
Refinement stepCycle: final / Resolution: 2.2→41.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4700 0 30 224 4954
Biso mean--21.95 31.32 -
Num. residues----573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094898
X-RAY DIFFRACTIONf_angle_d1.176675
X-RAY DIFFRACTIONf_chiral_restr0.083664
X-RAY DIFFRACTIONf_plane_restr0.006883
X-RAY DIFFRACTIONf_dihedral_angle_d15.6521785
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.26480.29711270.23412473260094
2.2648-2.33790.31341290.21532446257596
2.3379-2.42140.2741420.19992466260895
2.4214-2.51840.2761170.19612511262895
2.5184-2.6330.27641260.20872462258895
2.633-2.77180.24331490.19392487263696
2.7718-2.94540.27461260.19752506263298
2.9454-3.17270.25711270.2022603273099
3.1727-3.49190.25581280.205425972725100
3.4919-3.99680.21411530.18562580273399
3.9968-5.03420.20131470.15722510265795
5.0342-41.87930.20121490.17892637278699

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