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- PDB-5zre: Tyrosinase from Burkholderia thailandensis (BtTYR) at high pH con... -

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Basic information

Entry
Database: PDB / ID: 5zre
TitleTyrosinase from Burkholderia thailandensis (BtTYR) at high pH condition
ComponentsTyrosinase
KeywordsOXIDOREDUCTASE / Tyrosinase
Function / homology
Function and homology information


tyrosinase / tyrosinase activity
Similarity search - Function
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
Similarity search - Domain/homology
COPPER (II) ION / OXYGEN ATOM / Tyrosinase (Monophenol monooxygenase)
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsLee, S. / Son, H.-F. / Kim, K.-J.
CitationJournal: Acs Catalysis / Year: 2018
Title: Structural Basis for Highly Efficient Production of Catechol Derivatives at Acidic pH by Tyrosinase from Burkholderia thailandensis
Authors: Son, H.F. / Lee, S.H. / Lee, S.H. / Kim, H. / Hong, H. / Lee, U.J. / Lee, P.G. / Kim, B.G. / Kim, K.J.
History
DepositionApr 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosinase
B: Tyrosinase
C: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,54613
Polymers182,0253
Non-polymers52110
Water2,162120
1
A: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8184
Polymers60,6751
Non-polymers1433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9105
Polymers60,6751
Non-polymers2354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8184
Polymers60,6751
Non-polymers1433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.781, 72.175, 117.409
Angle α, β, γ (deg.)90.000, 105.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosinase / / Tyrosinase (Monophenol monooxygenase)


Mass: 60674.969 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264) (bacteria)
Strain: ATCC 700388 / DSM 13276 / CIP 106301 / E264 / Gene: melO, BTH_II0649, DR63_5120 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2T7K1, tyrosinase
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 18% (w/v) polyethyleneglycol 3350, 275 mM Ammonium iodide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→113.3 Å / Num. obs: 59146 / % possible obs: 97 % / Redundancy: 5.1 % / Rsym value: 0.122 / Net I/σ(I): 40.21
Reflection shellResolution: 2.5→2.54 Å / Rsym value: 0.307

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.5→27.85 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.901 / SU B: 10.196 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.511 / ESU R Free: 0.303
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 2948 5 %RANDOM
Rwork0.1993 ---
obs0.2026 56194 95.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 170.19 Å2 / Biso mean: 54.795 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.41 Å2-0 Å2-0.8 Å2
2--4.9 Å20 Å2
3----1.78 Å2
Refinement stepCycle: final / Resolution: 2.5→27.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11079 0 15 120 11214
Biso mean--50.8 46.7 -
Num. residues----1415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01511376
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710064
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.77815449
X-RAY DIFFRACTIONr_angle_other_deg0.5261.73123644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.24651396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36221.484512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55151676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0751564
X-RAY DIFFRACTIONr_chiral_restr0.070.21451
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022104
LS refinement shellResolution: 2.499→2.564 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 175 -
Rwork0.257 3294 -
all-3469 -
obs--76.87 %

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