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

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Basic information

Entry
Database: PDB / ID: 3ntm
TitleCrystal Structure of Tyrosinase from Bacillus megaterium crystallized in the absence of zinc, partial occupancy of CuB
ComponentsTyrosinase
KeywordsOXIDOREDUCTASE / tyrosinase / type3 copper proteins / Bacillus megaterium
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 / molecular replacement / Resolution: 2.3 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
DepositionJul 5, 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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Assembly

Deposited unit
A: Tyrosinase
B: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7605
Polymers70,5692
Non-polymers1913
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-7 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.010, 78.480, 74.550
Angle α, β, γ (deg.)90.00, 101.61, 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.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 1.87 Å3/Da / Density % sol: 34.16 %
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: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→73.025 Å / Num. all: 22077 / Num. obs: 22077 / % possible obs: 95.5 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.3-2.4220.1873.80.187194
2.42-2.5720.1644.30.164195
2.57-2.7520.1255.70.125196.4
2.75-2.972.10.0927.80.092196.5
2.97-3.252.20.06310.60.063196.8
3.25-3.642.20.04615.10.046195.8
3.64-4.22.20.034190.034196
4.2-5.142.20.034180.034194.9
5.14-7.272.10.03616.60.036194.4
7.27-39.242.10.03317.80.033192.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.21 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å39.24 Å
Translation2.5 Å39.24 Å

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Processing

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

3nm8


Resolution: 2.3→39.083 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.36 / σ(F): 0.01 / Phase error: 27.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2887 1117 5.16 %
Rwork0.1932 --
obs0.1981 21647 93.39 %
all-23180 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.365 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0213 Å2-0 Å2-2.5672 Å2
2---6.8496 Å20 Å2
3---6.8283 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å / Luzzati sigma a obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4611 0 3 236 4850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014827
X-RAY DIFFRACTIONf_angle_d1.196579
X-RAY DIFFRACTIONf_dihedral_angle_d17.6081763
X-RAY DIFFRACTIONf_chiral_restr0.078657
X-RAY DIFFRACTIONf_plane_restr0.005873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40470.35931340.23982498X-RAY DIFFRACTION91
2.4047-2.53150.35381390.23172480X-RAY DIFFRACTION91
2.5315-2.690.31431530.22192483X-RAY DIFFRACTION92
2.69-2.89770.31651580.19642568X-RAY DIFFRACTION94
2.8977-3.18910.26431170.18892649X-RAY DIFFRACTION96
3.1891-3.65030.2561330.17772612X-RAY DIFFRACTION95
3.6503-4.59790.26851530.15852613X-RAY DIFFRACTION95
4.5979-39.08830.24081300.18292627X-RAY DIFFRACTION93

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