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- PDB-5i3b: Crystal Structure of tyrosinase from Bacillus megaterium with con... -

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Basic information

Entry
Database: PDB / ID: 5i3b
TitleCrystal Structure of tyrosinase from Bacillus megaterium with configuration B of hydroquinone inhibitor 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
benzene-1,4-diol / Tyrosinase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsKanteev, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_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)67,1269
Polymers66,5792
Non-polymers5477
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-51 kcal/mol
Surface area23070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.620, 74.420, 119.690
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 4:23 or resseq 25:104 or resseq...
21(chain B and (resseq 4:23 or resseq 25:104 or resseq...

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
11LYSLYSVALVAL(chain A and (resseq 4:23 or resseq 25:104 or resseq...AA4 - 231 - 20
12THRTHRSERSER(chain A and (resseq 4:23 or resseq 25:104 or resseq...AA25 - 10422 - 101
13SERSERGLYGLY(chain A and (resseq 4:23 or resseq 25:104 or resseq...AA106 - 134103 - 131
14TRPTRPTHRTHR(chain A and (resseq 4:23 or resseq 25:104 or resseq...AA136 - 156133 - 153
15GLUGLUHISHIS(chain A and (resseq 4:23 or resseq 25:104 or resseq...AA158 - 245155 - 242
16GLNGLNLEULEU(chain A and (resseq 4:23 or resseq 25:104 or resseq...AA248 - 290245 - 287
21LYSLYSVALVAL(chain B and (resseq 4:23 or resseq 25:104 or resseq...BB4 - 231 - 20
22THRTHRSERSER(chain B and (resseq 4:23 or resseq 25:104 or resseq...BB25 - 10422 - 101
23SERSERGLYGLY(chain B and (resseq 4:23 or resseq 25:104 or resseq...BB106 - 134103 - 131
24TRPTRPTHRTHR(chain B and (resseq 4:23 or resseq 25:104 or resseq...BB136 - 156133 - 153
25GLUGLUHISHIS(chain B and (resseq 4:23 or resseq 25:104 or resseq...BB158 - 245155 - 242
26GLNGLNLEULEU(chain B and (resseq 4:23 or resseq 25:104 or resseq...BB248 - 290245 - 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HQE / benzene-1,4-diol


Mass: 110.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.33 Å3/Da / Density % sol: 47.18 % / Mosaicity: 0.58 °
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: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.2→63.2 Å / Num. all: 32260 / Num. obs: 32260 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 28.01 Å2 / Rpim(I) all: 0.033 / Rrim(I) all: 0.087 / Rsym value: 0.08 / Net I/av σ(I): 7.909 / Net I/σ(I): 15.4 / Num. measured all: 214516
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.326.90.3262.33236646590.1320.3530.3265.899.9
2.32-2.466.60.2413.12884743660.10.2610.2417.299.8
2.46-2.636.20.1784.12536441220.0770.1950.1788.499.7
2.63-2.8470.1365.32724538730.0550.1470.13611.9100
2.84-3.116.90.1016.92456135660.0410.1090.10115.6100
3.11-3.486.20.0778.92017232500.0330.0840.07719.599.9
3.48-4.027.10.05512.22052028830.0220.060.05527.899.9
4.02-4.926.20.04913.51529324630.0210.0540.04928.999.8
4.92-6.966.80.04514.41327919440.0180.0490.04527.599.9
6.96-33.4256.10.04612.2686911340.020.0510.0462999.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.28 Å33.43 Å
Translation5.28 Å33.43 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata reduction
SCALA3.3.22data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4p6r

4p6r


Resolution: 2.2→33.425 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2169 1636 5.08 %
Rwork0.1856 30573 -
obs0.1872 32209 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.35 Å2 / Biso mean: 32.8708 Å2 / Biso min: 14.1 Å2
Refinement stepCycle: final / Resolution: 2.2→33.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 21 266 4995
Biso mean--29.21 35.42 -
Num. residues----574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034880
X-RAY DIFFRACTIONf_angle_d0.6336648
X-RAY DIFFRACTIONf_chiral_restr0.043664
X-RAY DIFFRACTIONf_plane_restr0.004882
X-RAY DIFFRACTIONf_dihedral_angle_d17.2851780
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2738X-RAY DIFFRACTION5.054TORSIONAL
12B2738X-RAY DIFFRACTION5.054TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2001-2.26480.29371450.228625072652
2.2648-2.33790.26831250.218424972622
2.3379-2.42140.25591440.207325202664
2.4214-2.51830.21631320.204624902622
2.5183-2.63290.27631390.206325002639
2.6329-2.77160.22011460.202425352681
2.7716-2.94520.2471050.205325542659
2.9452-3.17240.26191410.202625342675
3.1724-3.49140.21391270.203425732700
3.4914-3.99590.191570.168825372694
3.9959-5.03160.1821230.149326192742
5.0316-33.4290.18381520.162127072859

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