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- PDB-4hd6: Crystal Structure of Tyrosinase from Bacillus megaterium V218F mu... -

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Basic information

Entry
Database: PDB / ID: 4hd6
TitleCrystal Structure of Tyrosinase from Bacillus megaterium V218F 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 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_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

Downloads & links

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Assembly

Deposited unit
A: Tyrosinase
B: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8596
Polymers70,6052
Non-polymers2544
Water4,576254
1
A: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4303
Polymers35,3031
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4303
Polymers35,3031
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.180, 78.910, 85.810
Angle α, β, γ (deg.)90.000, 106.130, 90.000
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, 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.: 254 / 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: 2.22 Å3/Da / Density % sol: 44.58 %
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→82.432 Å / Num. all: 40762 / Num. obs: 40762 / % possible obs: 97.5 % / Redundancy: 2.3 % / Rsym value: 0.074 / 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
2-2.112.30.28521339658920.28596.8
2.11-2.242.40.1763.61323256200.17698.1
2.24-2.392.30.1483.81184552500.14896.7
2.39-2.582.30.0976.11150249150.09798
2.58-2.832.30.0886.31043845580.08897.8
2.83-3.162.40.06210.1978540760.06297.3
3.16-3.652.40.0667.5864136480.06697.8
3.65-4.472.30.0618.5715730970.06198.5
4.47-6.322.50.05111605423990.05198.6
6.32-41.2162.50.04611.5330213070.04694.2

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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→41.216 Å / Occupancy max: 1 / Occupancy min: 0.55 / SU ML: 0.31 / σ(F): 1.33 / Phase error: 30.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2773 4068 10.02 %
Rwork0.2448 --
obs0.248 40605 97.15 %
all-40762 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.916 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso max: 140.07 Å2 / Biso mean: 25.902 Å2 / Biso min: 7.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.3602 Å2-0 Å25.5002 Å2
2---5.3994 Å2-0 Å2
3---8.7596 Å2
Refinement stepCycle: LAST / Resolution: 2→41.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 4 254 4966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124882
X-RAY DIFFRACTIONf_angle_d1.2446653
X-RAY DIFFRACTIONf_chiral_restr0.087660
X-RAY DIFFRACTIONf_plane_restr0.008881
X-RAY DIFFRACTIONf_dihedral_angle_d16.9831779
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02360.40361550.31171242139799
2.0236-2.04820.36331260.33941319144599
2.0482-2.07420.40491470.35451199134694
2.0742-2.10140.43791200.38061186130690
2.1014-2.13020.35491170.32121248136599
2.1302-2.16070.34511340.31971285141998
2.1607-2.19290.33181440.30821311145598
2.1929-2.22720.36971470.3141213136098
2.2272-2.26370.37811370.35631195133292
2.2637-2.30270.38381520.32651228138096
2.3027-2.34460.37331410.28321240138198
2.3446-2.38970.33051360.26321308144498
2.3897-2.43840.32881680.27831235140399
2.4384-2.49150.34411300.25961264139498
2.4915-2.54940.29851430.26061276141998
2.5494-2.61320.30121370.25521256139398
2.6132-2.68380.29051250.27261281140698
2.6838-2.76280.29031250.26891271139698
2.7628-2.85190.27991380.25661290142897
2.8519-2.95380.28481580.23981257141599
2.9538-3.0720.25791450.23581265141097
3.072-3.21180.29391440.24431240138496
3.2118-3.38110.25811440.23621253139798
3.3811-3.59280.24421700.23621241141197
3.5928-3.870.24421330.20881279141298
3.87-4.25910.21011350.19331280141597
4.2591-4.87450.16671330.16571305143898
4.8745-6.13820.19871350.181331146699
6.1382-41.22480.22211490.20171239138894

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