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- PDB-4p6s: Crystal Structure of tyrosinase from Bacillus megaterium with L-D... -

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Basic information

Entry
Database: PDB / ID: 4p6s
TitleCrystal Structure of tyrosinase from Bacillus megaterium with L-DOPA in the active site
ComponentsTyrosinase
KeywordsOXIDOREDUCTASE / L-DOPA / 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
3,4-DIHYDROXYPHENYLALANINE / 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 / _software.classification
Revision 1.3Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.4Dec 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _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)67,76012
Polymers66,5792
Non-polymers1,18110
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.880, 81.550, 84.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-DAH / 3,4-DIHYDROXYPHENYLALANINE / L-DOPA


Type: L-peptide linking / Mass: 197.188 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO4 / Comment: neurotransmitter*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.03 Å3/Da / Density % sol: 39.42 %
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→58.532 Å / Num. all: 28169 / Num. obs: 28169 / % possible obs: 99.8 % / Redundancy: 8.1 % / Biso Wilson estimate: 25.76 Å2 / Rpim(I) all: 0.039 / Rrim(I) all: 0.112 / Rsym value: 0.104 / Net I/av σ(I): 5.809 / Net I/σ(I): 13.1 / Num. measured all: 228410
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
2.2-2.3280.38223219040320.1420.382599.4
2.32-2.468.10.2832.73087538170.1050.2836.299.8
2.46-2.638.20.223.52998736390.0810.227.899.9
2.63-2.848.40.164.62805833540.0590.1610.2100
2.84-3.118.40.1195.92612731240.0440.11913.5100
3.11-3.488.20.0986.62329128250.0360.09817.2100
3.48-4.0280.0827.82026925240.0310.08221.8100
4.02-4.927.40.0699.31598921640.0270.06923.4100
4.92-6.968.10.0698.81382516980.0260.06923.6100
6.96-47.0047.90.05211.977999920.0190.05225.599

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.004 Å / FOM work R set: 0.8416 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2216 1414 5.03 %
Rwork0.1919 26698 -
obs0.1934 28112 99.77 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.082 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso max: 107.53 Å2 / Biso mean: 33.56 Å2 / Biso min: 10.11 Å2
Baniso -1Baniso -2Baniso -3
1--4.7882 Å2-0 Å20 Å2
2---8.5166 Å2-0 Å2
3---13.3047 Å2
Refinement stepCycle: final / Resolution: 2.2→47.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4699 0 82 251 5032
Biso mean--51.19 38.53 -
Num. residues----573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0294949
X-RAY DIFFRACTIONf_angle_d1.7076742
X-RAY DIFFRACTIONf_chiral_restr0.122669
X-RAY DIFFRACTIONf_plane_restr0.007890
X-RAY DIFFRACTIONf_dihedral_angle_d16.0821795
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.27860.29221320.24812615274799
2.2786-2.36990.29051510.234925952746100
2.3699-2.47770.2431340.225126582792100
2.4777-2.60830.24611230.220326462769100
2.6083-2.77170.24611270.214226542781100
2.7717-2.98570.25141470.209126592806100
2.9857-3.28610.24981560.194426482804100
3.2861-3.76150.21061390.183626852824100
3.7615-4.73830.18551490.156327172866100
4.7383-47.01520.1781560.171128212977100
Refinement TLS params.Method: refined / Origin x: -27.7861 Å / Origin y: -8.1233 Å / Origin z: 0.5128 Å
111213212223313233
T0.1009 Å2-0.0014 Å2-0.0185 Å2-0.1279 Å2-0.0197 Å2--0.0719 Å2
L0.9516 °20.0525 °20.1245 °2-1.9199 °2-0.1546 °2--0.3849 °2
S0.0518 Å °0.0145 Å °-0.131 Å °0.034 Å °-0.0044 Å °-0.1113 Å °0.1079 Å °0.0212 Å °-0.0393 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 290
2X-RAY DIFFRACTION1allB4 - 290
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allF1
7X-RAY DIFFRACTION1allI1
8X-RAY DIFFRACTION1allJ351
9X-RAY DIFFRACTION1allK352
10X-RAY DIFFRACTION1allL1
11X-RAY DIFFRACTION1allS1 - 272
12X-RAY DIFFRACTION1allG351
13X-RAY DIFFRACTION1allH351

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