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- PDB-7cit: Crystal structure of tyrosinase from Streptomyces castaneoglobisp... -

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Entry
Database: PDB / ID: 7cit
TitleCrystal structure of tyrosinase from Streptomyces castaneoglobisporus in complex with the caddie protein obtained by soaking in the solution containing Cu(II) and hydroxylamine for 24 h
Components
  • MelC
  • Tyrosinase
KeywordsMETAL BINDING PROTEIN / tyrosinase / catalytic mechanism
Function / homologyCOPPER (II) ION / NITRATE ION / HYDROGEN PEROXIDE
Function and homology information
Biological speciesStreptomyces castaneoglobisporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
Model detailsTyr98 residue of caddie is partially oxygenated
AuthorsOda, K. / Matoba, Y.
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: The basicity of an active-site water molecule discriminates between tyrosinase and catechol oxidase activity.
Authors: Matoba, Y. / Oda, K. / Muraki, Y. / Masuda, T.
History
DepositionJul 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 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 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosinase
B: MelC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,03114
Polymers46,3072
Non-polymers72412
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-55 kcal/mol
Surface area13420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.560, 96.080, 54.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-304-

CU

21A-578-

HOH

31A-581-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Tyrosinase


Mass: 32089.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces castaneoglobisporus (bacteria)
Strain: HUT 6202 / Plasmid: PET-MEL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLYSS
#2: Protein MelC


Mass: 14217.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces castaneoglobisporus (bacteria)
Strain: HUT 6202 / Plasmid: PET-MEL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLYSS

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Non-polymers , 4 types, 335 molecules

#3: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.84 Å3/Da / Density % sol: 32.61 % / Mosaicity: 0.824 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 3350, NaNO3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→100 Å / Num. obs: 53168 / % possible obs: 96.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.049 / Χ2: 0.982 / Net I/σ(I): 35.6
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.432 / Num. unique obs: 5762 / Χ2: 1.176

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Processing

Software
NameVersionClassification
SHELXrefinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZMY

2zmy


Resolution: 1.5→30 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.2067 2614 -RANDOM
Rwork0.1438 ---
obs0.1438 53111 96.3 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso max: 129.37 Å2 / Biso mean: 25.7909 Å2 / Biso min: 12.19 Å2
Refinement stepCycle: final / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 36 322 3180
Biso mean--37.75 41.21 -
Num. residues----354
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.031
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.363
X-RAY DIFFRACTIONs_zero_chiral_vol0.05
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.061
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.017
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.03
X-RAY DIFFRACTIONs_approx_iso_adps0.133

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