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- PDB-8hpi: Crystal structure of Tyrosinase from Priestia megaterium -

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Basic information

Entry
Database: PDB / ID: 8hpi
TitleCrystal structure of Tyrosinase from Priestia megaterium
ComponentsTyrosinase
KeywordsOXIDOREDUCTASE / Tyrosinase Priestia megaterium
Function / homologyTyrosinase 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 / oxidoreductase activity / metal ion binding / Tyrosinase
Function and homology information
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsHuang, Y. / Song, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Tyrosinase from Priestia megaterium
Authors: Huang, Y. / Song, W.
History
DepositionDec 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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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)68,09823
Polymers66,7452
Non-polymers1,35421
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-467 kcal/mol
Surface area22620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.950, 104.950, 137.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Tyrosinase


Mass: 33372.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (strain WSH-002) (bacteria)
Gene: melC1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A8D3X086
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.85 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: PEG 4000, Zinc acetate dehydrate, Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54184 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: May 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.54→46.94 Å / Num. obs: 39392 / % possible obs: 99.4 % / Redundancy: 4.5 % / CC1/2: 0.993 / Net I/σ(I): 4.08
Reflection shellResolution: 2.54→2.65 Å / Num. unique obs: 3 / CC1/2: 0.584

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Processing

SoftwareName: Aimless / Classification: data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→46.98 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.898 / SU B: 10.619 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.541 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24909 1340 5.3 %RANDOM
Rwork0.19986 ---
obs0.20238 24148 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.934 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å2-0 Å2-0 Å2
2--1.19 Å20 Å2
3----2.38 Å2
Refinement stepCycle: 1 / Resolution: 2.54→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 39 153 4900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134916
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154416
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.6596669
X-RAY DIFFRACTIONr_angle_other_deg1.1811.58410145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8475574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.18521.839299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.23915750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2271538
X-RAY DIFFRACTIONr_chiral_restr0.0610.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025620
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021248
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0163.4282302
X-RAY DIFFRACTIONr_mcbond_other2.0153.4272301
X-RAY DIFFRACTIONr_mcangle_it3.2545.1352874
X-RAY DIFFRACTIONr_mcangle_other3.2545.1362875
X-RAY DIFFRACTIONr_scbond_it2.5853.6672614
X-RAY DIFFRACTIONr_scbond_other2.5843.6672615
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7765.3613796
X-RAY DIFFRACTIONr_long_range_B_refined5.66638.9245661
X-RAY DIFFRACTIONr_long_range_B_other5.66338.9465636
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10198 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.541→2.607 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 87 -
Rwork0.311 1699 -
obs--93.85 %

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