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- PDB-3nq0: Crystal Structure of Tyrosinase from Bacillus megaterium crystall... -

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Basic information

Entry
Database: PDB / ID: 3nq0
TitleCrystal Structure of Tyrosinase from Bacillus megaterium crystallized in the absence of Zinc
ComponentsTyrosinase
KeywordsOXIDOREDUCTASE / tyrosinase / type3 copper proteins / Bacillus megaterium
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: 2.2 Å
AuthorsSendovski, M. / Kanteev, M. / Adir, N. / Fishman, A.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: First structures of an active bacterial tyrosinase reveal copper plasticity.
Authors: Sendovski, M. / Kanteev, M. / Shuster Ben-Yosef, V. / Adir, N. / Fishman, A.
#1: Journal: To be Published
Title: Crystallization and preliminary x-ray crystallographic analysis of a bacterial tyrosinase from Bacillus megaterium
Authors: Sendovski, M. / Kanteev, M. / Adir, N. / Fishman, A.
History
DepositionJun 29, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Nov 1, 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 / 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_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.ptnr1_label_seq_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.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)70,6964
Polymers70,5692
Non-polymers1272
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.820, 78.700, 85.580
Angle α, β, γ (deg.)90.00, 105.29, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→82.551 Å / Num. all: 31201 / Num. obs: 29606 / % possible obs: 95.1 % / Redundancy: 2.1 % / Biso Wilson estimate: 12.4 Å2 / Rsym value: 0.1 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.2-2.321.90.3342.20.334187.3
2.32-2.462.10.2682.70.268197
2.46-2.632.10.223.30.22197.1
2.63-2.842.10.1684.20.168196.9
2.84-3.112.10.1166.10.116195.8
3.11-3.482.10.0759.30.075196
3.48-4.022.10.0513.20.05196.3
4.02-4.922.10.0415.90.04196.5
4.92-6.962.10.04116.30.041195.7
6.96-41.27520.03216.60.032193.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 37.64 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å41.28 Å
Translation3.5 Å41.28 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
DNAdata collection
PHENIX1.6.1_357refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NM8

3nm8


Resolution: 2.2→41.275 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.36 / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2916 1424 5.1 %
Rwork0.2425 --
obs0.245 27907 89.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.351 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 17.4718 Å2
Baniso -1Baniso -2Baniso -3
1-3.7913 Å20 Å24.57 Å2
2---4.6285 Å20 Å2
3---0.8371 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å / Luzzati sigma a obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.2→41.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4596 0 2 159 4757
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009723
X-RAY DIFFRACTIONf_angle_d1.48226
X-RAY DIFFRACTIONf_dihedral_angle_d22.26
X-RAY DIFFRACTIONf_chiral_restr
X-RAY DIFFRACTIONf_plane_restr

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