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- PDB-4hd4: Crystal Structure of Tyrosinase from Bacillus megaterium V218F mutant -

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Basic information

Entry
Database: PDB / ID: 4hd4
TitleCrystal Structure of Tyrosinase from Bacillus megaterium V218F mutant
ComponentsTyrosinase
KeywordsOXIDOREDUCTASE / tyrosinase / type 3 copper protein
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: 1.8 Å
AuthorsGoldfeder, M. / Kanteev, M. / Adir, N. / Fishman, A.
Citation
Journal: Biochim.Biophys.Acta / Year: 2013
Title: Influencing the monophenolase/diphenolase activity ratio in tyrosinase.
Authors: Goldfeder, M. / Kanteev, 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
DepositionOct 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Feb 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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

Downloads & links

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Assembly

Deposited unit
A: Tyrosinase
B: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7324
Polymers70,6052
Non-polymers1272
Water4,252236
1
A: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3662
Polymers35,3031
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3662
Polymers35,3031
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.000, 78.580, 85.890
Angle α, β, γ (deg.)90.00, 106.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosinase


Mass: 35302.520 Da / Num. of mol.: 2 / Mutation: S2G, V218F
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
#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.: 236 / 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: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, sodium cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorDate: Feb 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→36.53 Å / Num. all: 54388 / Num. obs: 54388 / % possible obs: 96.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.099
Reflection shellResolution: 1.8→1.9 Å / % possible all: 96.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→28.451 Å / Occupancy max: 1.2 / Occupancy min: 0.24 / SU ML: 0.2 / σ(F): 1.34 / Phase error: 22.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2284 5457 10.04 %
Rwork0.2066 --
obs0.2088 54339 95.62 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.408 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3479 Å20 Å21.4876 Å2
2---3.75 Å2-0 Å2
3---0.3924 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 2 236 4946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014884
X-RAY DIFFRACTIONf_angle_d1.2226653
X-RAY DIFFRACTIONf_dihedral_angle_d16.1351783
X-RAY DIFFRACTIONf_chiral_restr0.096661
X-RAY DIFFRACTIONf_plane_restr0.006884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.28351860.22761636X-RAY DIFFRACTION96
1.8205-1.84190.25111760.21551631X-RAY DIFFRACTION96
1.8419-1.86430.24231680.21871624X-RAY DIFFRACTION96
1.8643-1.88790.24851700.21581622X-RAY DIFFRACTION96
1.8879-1.91280.2551920.22511676X-RAY DIFFRACTION97
1.9128-1.9390.26431930.20951579X-RAY DIFFRACTION96
1.939-1.96670.27991810.21251640X-RAY DIFFRACTION96
1.9667-1.9960.25541750.21581659X-RAY DIFFRACTION97
1.996-2.02720.24312110.23221571X-RAY DIFFRACTION97
2.0272-2.06040.25941850.22141654X-RAY DIFFRACTION97
2.0604-2.09590.26921940.23251665X-RAY DIFFRACTION97
2.0959-2.1340.24521750.22181617X-RAY DIFFRACTION97
2.134-2.17510.23451800.2181690X-RAY DIFFRACTION97
2.1751-2.21950.22931960.20971595X-RAY DIFFRACTION97
2.2195-2.26770.24161760.20531670X-RAY DIFFRACTION97
2.2677-2.32040.2331940.21511648X-RAY DIFFRACTION97
2.3204-2.37840.21681760.21021669X-RAY DIFFRACTION97
2.3784-2.44270.23771700.21191621X-RAY DIFFRACTION97
2.4427-2.51450.252100.21791645X-RAY DIFFRACTION97
2.5145-2.59560.26561860.21961652X-RAY DIFFRACTION97
2.5956-2.68840.2481740.21911667X-RAY DIFFRACTION97
2.6884-2.79590.23351650.22741649X-RAY DIFFRACTION97
2.7959-2.9230.20871620.21161647X-RAY DIFFRACTION96
2.923-3.0770.24171730.2131655X-RAY DIFFRACTION96
3.077-3.26950.23381960.21821618X-RAY DIFFRACTION95
3.2695-3.52150.2331980.2111604X-RAY DIFFRACTION94
3.5215-3.87510.20961870.18621622X-RAY DIFFRACTION95
3.8751-4.4340.18351760.16311605X-RAY DIFFRACTION93
4.434-5.57950.15871750.16471596X-RAY DIFFRACTION92
5.5795-28.45490.17971570.18791455X-RAY DIFFRACTION82

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