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- PDB-6z1s: Structure of Polyphenol Oxidase (mutant G292N) from Thermothelomy... -

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Basic information

Entry
Database: PDB / ID: 6z1s
TitleStructure of Polyphenol Oxidase (mutant G292N) from Thermothelomyces thermophila
ComponentsTyrosinase-like protein
KeywordsOXIDOREDUCTASE / polyphenol oxidase / melanin synthesis / dicopper center / extracellular
Function / homology
Function and homology information


monooxygenase activity / metal ion binding
Similarity search - Function
di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / : / 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 / GLYCINE / SERINE / Tyrosinase-like protein
Similarity search - Component
Biological speciesThermothelomyces thermophilus ATCC 42464 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsDimarogona, M. / Nikolaivits, E. / Valmas, A. / Topakas, E.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)653706European Union
CitationJournal: Appl.Environ.Microbiol. / Year: 2021
Title: Considerations Regarding Activity Determinants of Fungal Polyphenol Oxidases Based on Mutational and Structural Studies.
Authors: Nikolaivits, E. / Valmas, A. / Dedes, G. / Topakas, E. / Dimarogona, M.
History
DepositionMay 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_contact_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosinase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,24114
Polymers46,5741
Non-polymers1,66813
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-21 kcal/mol
Surface area15750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.404, 97.177, 46.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Tyrosinase-like protein


Mass: 46573.566 Da / Num. of mol.: 1 / Mutation: G292N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermothelomyces thermophilus ATCC 42464 (fungus)
Gene: MYCTH_60685 / Production host: Komagataella pastoris (fungus) / References: UniProt: G2QLD3

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Sugars , 2 types, 3 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 369 molecules

#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H5NO2
#6: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#7: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cu
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1
Details: crystallization and data collection were performed by the HTX lab at EMBL Grenoble and that the crystals were automatically harvested and cryocooled with the CrystalDirect technology

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Moprheus buffer 3, amino acids mix, MPD, PEG1000, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.98012 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98012 Å / Relative weight: 1
ReflectionResolution: 1.53→43.24 Å / Num. obs: 30047 / % possible obs: 86.3 % / Redundancy: 13.3 % / CC1/2: 0.999 / Net I/σ(I): 12.4
Reflection shellResolution: 1.554→1.719 Å / Num. unique obs: 1502 / CC1/2: 0.605

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
autoPROC1.1.7data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J3Q

4j3q


Resolution: 1.53→43.24 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.062 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20659 1478 4.9 %RANDOM
Rwork0.15743 ---
obs0.15989 28590 49.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.138 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.3 Å2
Refinement stepCycle: 1 / Resolution: 1.53→43.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2964 0 102 359 3425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133173
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172817
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.694328
X-RAY DIFFRACTIONr_angle_other_deg1.3681.6096545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6785383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.20921.506166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76615441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7991522
X-RAY DIFFRACTIONr_chiral_restr0.0830.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023613
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02688
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_it1.8482.0571553
X-RAY DIFFRACTIONr_mcbond_other1.8222.0541551
X-RAY DIFFRACTIONr_mcangle_it2.83.0351926
X-RAY DIFFRACTIONr_mcangle_other2.8013.0351926
X-RAY DIFFRACTIONr_scbond_it2.3152.281620
X-RAY DIFFRACTIONr_scbond_other2.3152.281620
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6783.3452401
X-RAY DIFFRACTIONr_long_range_B_refined5.5524.6563784
X-RAY DIFFRACTIONr_long_range_B_other5.44524.2033694
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 5 -
Rwork0.38 55 -
obs--1.35 %

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