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- PDB-2p3x: Crystal structure of Grenache (Vitis vinifera) Polyphenol Oxidase -

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Basic information

Entry
Database: PDB / ID: 2p3x
TitleCrystal structure of Grenache (Vitis vinifera) Polyphenol Oxidase
ComponentsPolyphenol oxidase, chloroplast
KeywordsOXIDOREDUCTASE / Polyphenol oxidase / Grenache grapes
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 / Hemocyanin/hexamerin / 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 ...Polyphenol oxidase / Polyphenol oxidase, C-terminal / Protein of unknown function (DUF_B2219) / Polyphenol oxidase, central domain / Polyphenol oxidase middle domain / Hemocyanin/hexamerin / 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
CU-O-CU LINKAGE / Polyphenol oxidase, chloroplastic
Similarity search - Component
Biological speciesVitis vinifera (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsReyes Grajeda, J.P. / Virador, V.M. / Blanco-Labra, A. / Mendiola-Olaya, E. / Smith, G.M. / Moreno, A. / Whitaker, J.R.
CitationJournal: J.Agric.Food Chem. / Year: 2010
Title: Cloning, sequencing, purification, and crystal structure of Grenache (Vitis vinifera) polyphenol oxidase.
Authors: Virador, V.M. / Reyes Grajeda, J.P. / Blanco-Labra, A. / Mendiola-Olaya, E. / Smith, G.M. / Moreno, A. / Whitaker, J.R.
History
DepositionMar 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Polyphenol oxidase, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6112
Polymers38,4681
Non-polymers1431
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.030, 120.770, 140.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Polyphenol oxidase, chloroplast / PPO / Catechol oxidase


Mass: 38468.355 Da / Num. of mol.: 1 / Fragment: Polyphenol oxidase / Source method: isolated from a natural source / Details: grape berries / Source: (natural) Vitis vinifera (wine grape) / References: UniProt: P43311, catechol oxidase
#2: Chemical ChemComp-C2O / CU-O-CU LINKAGE


Mass: 143.091 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.31 Å3/Da / Density % sol: 62.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 19, 2006 / Details: Monochromator
RadiationMonochromator: Si(111) channel cut monochromator. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 26382 / Redundancy: 6.96 %
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.41 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.9 / Num. unique all: 26382 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
CrystalCleardata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Polyphenol oxidase of sweet potato (1BT1)

1bt1


Resolution: 2.2→37.06 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.703 / SU ML: 0.145 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25205 2598 9.9 %RANDOM
Rwork0.20053 ---
all0.2057 ---
obs0.20572 23748 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.449 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 3 128 2844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222803
X-RAY DIFFRACTIONr_angle_refined_deg2.5451.9553833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.1875338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53524.341129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.47415435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5071511
X-RAY DIFFRACTIONr_chiral_restr0.2770.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022186
X-RAY DIFFRACTIONr_nbd_refined0.2470.21291
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21828
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2139
X-RAY DIFFRACTIONr_metal_ion_refined0.010.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.23
X-RAY DIFFRACTIONr_mcbond_it1.3131.51758
X-RAY DIFFRACTIONr_mcangle_it2.15322778
X-RAY DIFFRACTIONr_scbond_it3.2731239
X-RAY DIFFRACTIONr_scangle_it4.8674.51055
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0.324 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 199 -
Rwork0.25 1670 -
obs-1670 97.24 %

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