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- PDB-4d87: Crystal Structure of Tyrosinase from Bacillus megaterium in compl... -

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Basic information

Entry
Database: PDB / ID: 4d87
TitleCrystal Structure of Tyrosinase from Bacillus megaterium in complex with SDS
ComponentsTyrosinase
KeywordsOXIDOREDUCTASE / type 3 copper protein / tyrosinase
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
COPPER (II) ION / Tyrosinase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsAdir, N. / Goldfeder, M. / Fishman, A.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2013
Title: Changes in tyrosinase specificity by ionic liquids and sodium dodecyl sulfate.
Authors: Goldfeder, M. / Egozy, M. / Shuster Ben-Yosef, V. / Adir, N. / Fishman, A.
History
DepositionJan 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 27, 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_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

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Assembly

Deposited unit
A: Tyrosinase
B: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9625
Polymers70,5692
Non-polymers3933
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6143
Polymers35,2851
Non-polymers3302
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3482
Polymers35,2851
Non-polymers641
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.840, 79.140, 85.930
Angle α, β, γ (deg.)90.00, 103.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosinase


Mass: 35284.500 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-SDS / DODECYL SULFATE


Mass: 266.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O4S / Comment: detergent*YM

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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: 2.24 Å3/Da / Density % sol: 45.11 %
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
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.5→83.53 Å / Num. all: 16950 / Num. obs: 6631 / % possible obs: 82.97 % / Rmerge(I) obs: 0.097
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.5-3.692.60.1627.8173.4
11.07-57.452.50.0589.7193.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→83.5 Å / Cor.coef. Fo:Fc: 0.771 / Cor.coef. Fo:Fc free: 0.691 / SU B: 0.007 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.886 / ESU R Free: 1.001 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29287 650 9.8 %RANDOM
Rwork0.25925 ---
obs0.26248 5980 82.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.976 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20.54 Å2
2---0.63 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 3.5→83.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4683 0 19 0 4702
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 50 -
Rwork0.334 411 -
obs--77.74 %

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