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- PDB-6hqj: apo-form of polyphenol oxidase from Solanum lycopersicum -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6hqj
Titleapo-form of polyphenol oxidase from Solanum lycopersicum
ComponentsPolyphenol oxidase A, chloroplastic
KeywordsOXIDOREDUCTASE / polyphenol oxidase / tyrosinase
Function / homology
Function and homology information


catechol oxidase / catechol oxidase activity / pigment biosynthetic process / chloroplast thylakoid lumen / metal ion binding
Similarity search - Function
Polyphenol oxidase / Polyphenol oxidase, C-terminal / Protein of unknown function (DUF_B2219) / Polyphenol oxidase, central domain / Polyphenol oxidase middle domain / 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
Polyphenol oxidase A, chloroplastic
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsKampatsikas, I. / Bijelic, A. / Rompel, A.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund29144 Austria
CitationJournal: Sci Rep / Year: 2019
Title: Biochemical and structural characterization of tomato polyphenol oxidases provide novel insights into their substrate specificity.
Authors: Kampatsikas, I. / Bijelic, A. / Rompel, A.
History
DepositionSep 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyphenol oxidase A, chloroplastic


Theoretical massNumber of molelcules
Total (without water)57,2181
Polymers57,2181
Non-polymers00
Water8,197455
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.800, 54.140, 69.770
Angle α, β, γ (deg.)90.00, 101.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polyphenol oxidase A, chloroplastic


Mass: 57218.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Production host: Escherichia coli (E. coli) / References: UniProt: Q08303*PLUS, catechol oxidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 50 mM sodium citrate pH 6.6, 13% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.8→42.47 Å / Num. obs: 40854 / % possible obs: 98.95 % / Redundancy: 3.1 % / Rpim(I) all: 0.049 / Net I/σ(I): 10.5
Reflection shellResolution: 1.8→1.87 Å / Rpim(I) all: 0.441

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HQI
Resolution: 1.802→42.468 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.07
RfactorNum. reflection% reflection
Rfree0.2006 2043 5 %
Rwork0.1637 --
obs0.1655 40853 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.802→42.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3736 0 0 455 4191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073825
X-RAY DIFFRACTIONf_angle_d0.8545197
X-RAY DIFFRACTIONf_dihedral_angle_d14.1062266
X-RAY DIFFRACTIONf_chiral_restr0.053546
X-RAY DIFFRACTIONf_plane_restr0.006685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8024-1.84430.29771320.28872511X-RAY DIFFRACTION97
1.8443-1.89040.28861340.24212542X-RAY DIFFRACTION99
1.8904-1.94150.25461370.22322606X-RAY DIFFRACTION99
1.9415-1.99870.24441340.20122555X-RAY DIFFRACTION99
1.9987-2.06320.22551370.18742591X-RAY DIFFRACTION99
2.0632-2.13690.24151360.18032589X-RAY DIFFRACTION99
2.1369-2.22250.19241340.17112541X-RAY DIFFRACTION98
2.2225-2.32360.21451380.16152622X-RAY DIFFRACTION100
2.3236-2.44610.20021360.15462594X-RAY DIFFRACTION100
2.4461-2.59930.21751370.16252598X-RAY DIFFRACTION100
2.5993-2.80.22011370.15772606X-RAY DIFFRACTION99
2.8-3.08170.20961360.16422587X-RAY DIFFRACTION99
3.0817-3.52740.20621370.15122604X-RAY DIFFRACTION99
3.5274-4.44340.1531380.1322616X-RAY DIFFRACTION99
4.4434-42.47950.15861400.14962648X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.73820.3604-0.12290.81120.02481.5499-0.02820.09180.0657-0.09570.02850.0146-0.11910.03620.00560.15580.00720.00480.16270.01290.186249.655428.059648.3486
21.10290.5754-0.2181.0536-0.43450.7631-0.05580.03880.0867-0.02410.05930.0875-0.0282-0.08110.03170.13420.0187-0.01060.15280.00050.188338.198521.986851.2911
32.8619-0.0902-0.04830.3935-0.09570.4244-0.0271-0.1149-0.0484-0.03790.04120.0829-0.0041-0.16210.0050.17240.00460.00640.186-0.00050.198320.544313.20256.7972
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 184 )
2X-RAY DIFFRACTION2chain 'A' and (resid 185 through 345 )
3X-RAY DIFFRACTION3chain 'A' and (resid 346 through 514 )

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