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- PDB-5i38: Crystal Structure of tyrosinase from Bacillus megaterium with inh... -

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Basic information

Entry
Database: PDB / ID: 5i38
TitleCrystal Structure of tyrosinase from Bacillus megaterium with inhibitor kojic acid in the active site
ComponentsTyrosinase
KeywordsOXIDOREDUCTASE / di-copper oxidase
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 / 5-HYDROXY-2-(HYDROXYMETHYL)-4H-PYRAN-4-ONE / Tyrosinase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsKanteev, M. / Goldfeder, M. / Deri, B. / Adir, N. / Fishman, A.
Funding support Israel, 1items
OrganizationGrant numberCountry
ISF419/15 Israel
CitationJournal: Sci Rep / Year: 2016
Title: The unravelling of the complex pattern of tyrosinase inhibition.
Authors: Deri, B. / Kanteev, M. / Goldfeder, M. / Lecina, D. / Guallar, V. / Adir, N. / Fishman, A.
History
DepositionFeb 10, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)67,1178
Polymers66,5792
Non-polymers5386
Water1,49583
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-62 kcal/mol
Surface area22880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.240, 74.970, 121.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 6:55 or (resid 56 and (name...
21(chain B and (resseq 6:55 or (resid 56 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGASPASP(chain A and (resseq 6:55 or (resid 56 and (name...AA6 - 553 - 52
12ARGARGARGARG(chain A and (resseq 6:55 or (resid 56 and (name...AA5653
13TYRTYRLEULEU(chain A and (resseq 6:55 or (resid 56 and (name...AA5 - 2902 - 287
14TYRTYRLEULEU(chain A and (resseq 6:55 or (resid 56 and (name...AA5 - 2902 - 287
15TYRTYRLEULEU(chain A and (resseq 6:55 or (resid 56 and (name...AA5 - 2902 - 287
16TYRTYRLEULEU(chain A and (resseq 6:55 or (resid 56 and (name...AA5 - 2902 - 287
17TYRTYRLEULEU(chain A and (resseq 6:55 or (resid 56 and (name...AA5 - 2902 - 287
18TYRTYRLEULEU(chain A and (resseq 6:55 or (resid 56 and (name...AA5 - 2902 - 287
19TYRTYRLEULEU(chain A and (resseq 6:55 or (resid 56 and (name...AA5 - 2902 - 287
110TYRTYRLEULEU(chain A and (resseq 6:55 or (resid 56 and (name...AA5 - 2902 - 287
111TYRTYRLEULEU(chain A and (resseq 6:55 or (resid 56 and (name...AA5 - 2902 - 287
21ARGARGASPASP(chain B and (resseq 6:55 or (resid 56 and (name...BB6 - 553 - 52
22ARGARGARGARG(chain B and (resseq 6:55 or (resid 56 and (name...BB5653
23LYSLYSLEULEU(chain B and (resseq 6:55 or (resid 56 and (name...BB4 - 2901 - 287
24LYSLYSLEULEU(chain B and (resseq 6:55 or (resid 56 and (name...BB4 - 2901 - 287
25LYSLYSLEULEU(chain B and (resseq 6:55 or (resid 56 and (name...BB4 - 2901 - 287
26LYSLYSLEULEU(chain B and (resseq 6:55 or (resid 56 and (name...BB4 - 2901 - 287
27LYSLYSLEULEU(chain B and (resseq 6:55 or (resid 56 and (name...BB4 - 2901 - 287
28LYSLYSLEULEU(chain B and (resseq 6:55 or (resid 56 and (name...BB4 - 2901 - 287
29LYSLYSLEULEU(chain B and (resseq 6:55 or (resid 56 and (name...BB4 - 2901 - 287
210LYSLYSLEULEU(chain B and (resseq 6:55 or (resid 56 and (name...BB4 - 2901 - 287
211LYSLYSLEULEU(chain B and (resseq 6:55 or (resid 56 and (name...BB4 - 2901 - 287

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Components

#1: Protein Tyrosinase


Mass: 33289.266 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 BL21(DE3) (bacteria) / References: UniProt: B2ZB02
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-KOJ / 5-HYDROXY-2-(HYDROXYMETHYL)-4H-PYRAN-4-ONE


Mass: 142.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG8000, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93936 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93936 Å / Relative weight: 1
ReflectionResolution: 2.5→63.831 Å / Num. obs: 20671 / % possible obs: 90.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 30.64 Å2 / Rsym value: 0.127 / Net I/av σ(I): 3.128 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.5-2.645.80.2522.5199.3
2.64-2.85.40.31173.4
2.8-2.996.40.1574.11100
2.99-3.236.70.1364.71100
3.23-3.546.10.2031.6184.1
3.54-3.955.90.1512.9164.2
3.95-4.566.20.16.4199.6
4.56-5.595.80.0837.8199.7
5.59-7.917.50.0778.41100
7.91-40.5676.50.0827.6186.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å35.82 Å
Translation2.5 Å35.82 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASER2.3.0phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P6R

4p6r


Resolution: 2.6→35.824 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.61
RfactorNum. reflection% reflection
Rfree0.2406 914 5.05 %
Rwork0.2081 --
obs0.2097 18103 88.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.94 Å2 / Biso mean: 32.0231 Å2 / Biso min: 10.19 Å2
Refinement stepCycle: final / Resolution: 2.6→35.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4699 0 24 83 4806
Biso mean--33.51 30.74 -
Num. residues----573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024875
X-RAY DIFFRACTIONf_angle_d0.5216643
X-RAY DIFFRACTIONf_chiral_restr0.04663
X-RAY DIFFRACTIONf_plane_restr0.004881
X-RAY DIFFRACTIONf_dihedral_angle_d11.6582839
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2726X-RAY DIFFRACTION3.875TORSIONAL
12B2726X-RAY DIFFRACTION3.875TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.7370.37181040.29781858196269
2.737-2.90840.26931490.239427252874100
2.9084-3.13290.25351350.226227352870100
3.1329-3.44790.26861510.23332454260599
3.4479-3.94630.251050.22771822192769
3.9463-4.96980.18411400.16382771291199
4.9698-35.82750.21811300.18582824295496

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