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- PDB-4hd7: Crystal Structure of Tyrosinase from Bacillus megaterium V218G mu... -

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Basic information

Entry
Database: PDB / ID: 4hd7
TitleCrystal Structure of Tyrosinase from Bacillus megaterium V218G mutant soaked in CuSO4
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: 2.1 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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)70,6796
Polymers70,4252
Non-polymers2544
Water3,855214
1
A: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3393
Polymers35,2121
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3393
Polymers35,2121
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.900, 78.670, 85.770
Angle α, β, γ (deg.)90.000, 105.910, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosinase


Mass: 35212.395 Da / Num. of mol.: 2 / Mutation: S2G, V218G
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.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
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: 2.1→82.484 Å / Num. all: 34263 / Num. obs: 34263 / % possible obs: 95.9 % / Redundancy: 2.4 % / Rsym value: 0.087 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.212.40.1813.51229850920.18198.3
2.21-2.352.30.2461.11091447510.24696.8
2.35-2.512.40.1065.51105245300.10697.4
2.51-2.712.40.133.1991841970.1396.9
2.71-2.972.40.0747.5926937930.07496.1
2.97-3.322.50.0599.8845134410.05995.7
3.32-3.832.40.0884.7708430050.08894.6
3.83-4.72.30.0647.6585325010.06493.1
4.7-6.642.30.05210.6445619600.05293.6
6.64-41.2422.50.03616.825039930.03685.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→36.214 Å / Occupancy max: 1 / Occupancy min: 0.34 / SU ML: 0.29 / σ(F): 1.37 / Phase error: 30.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2821 3427 10.03 %
Rwork0.2537 --
obs0.2566 34184 95.38 %
all-34263 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.919 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 137.58 Å2 / Biso mean: 26.3701 Å2 / Biso min: 5.94 Å2
Baniso -1Baniso -2Baniso -3
1-5.716 Å2-0 Å2-9.4238 Å2
2---9.0141 Å20 Å2
3---3.2982 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4686 0 4 214 4904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124870
X-RAY DIFFRACTIONf_angle_d1.2146638
X-RAY DIFFRACTIONf_chiral_restr0.09657
X-RAY DIFFRACTIONf_plane_restr0.006881
X-RAY DIFFRACTIONf_dihedral_angle_d16.8971776
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.130.34161350.28631296143198
2.13-2.16180.31721430.27121320146398
2.1618-2.19560.35891470.27651334148198
2.1956-2.23160.32121410.30251288142998
2.2316-2.270.54461460.50951231137792
2.27-2.31130.36871390.3061301144097
2.3113-2.35580.32971310.27141308143997
2.3558-2.40380.31811450.24721310145597
2.4038-2.45610.2921360.26081319145598
2.4561-2.51320.35231460.24621288143497
2.5132-2.5760.29241460.27041286143297
2.576-2.64570.30741280.27861331145996
2.6457-2.72350.37851440.35151255139996
2.7235-2.81140.29981380.27291332147096
2.8114-2.91180.29641340.2491275140996
2.9118-3.02830.25931500.23261271142195
3.0283-3.16610.28621500.23491286143696
3.1661-3.33290.25851500.23851265141595
3.3329-3.54160.2871570.28711270142794
3.5416-3.81470.23391520.22881235138794
3.8147-4.19810.22481420.20381255139793
4.1981-4.80440.17911400.16281257139792
4.8044-6.04840.20581500.1891255140593
6.0484-36.21910.22831370.20431189132686

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