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- PDB-1xg2: Crystal structure of the complex between pectin methylesterase an... -

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Basic information

Entry
Database: PDB / ID: 1xg2
TitleCrystal structure of the complex between pectin methylesterase and its inhibitor protein
Components
  • Pectinesterase 1
  • Pectinesterase inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEIN-PROTEIN COMPLEX / BETA HELIX / FOUR HELIX BUNDLE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


pectinesterase inhibitor activity / fruit ripening / pectinesterase / pectinesterase activity / cell wall modification / pectin catabolic process / extracellular region / cytoplasm
Similarity search - Function
Pectinesterase, Tyr active site / Pectinesterase signature 1. / Pectinesterase inhibitor, plant / : / Invertase/pectin methylesterase inhibitor family protein / Pectinesterase inhibitor domain / Invertase/pectin methylesterase inhibitor domain superfamily / Plant invertase/pectin methylesterase inhibitor / Plant invertase/pectin methylesterase inhibitor / Pectinesterase, Asp active site ...Pectinesterase, Tyr active site / Pectinesterase signature 1. / Pectinesterase inhibitor, plant / : / Invertase/pectin methylesterase inhibitor family protein / Pectinesterase inhibitor domain / Invertase/pectin methylesterase inhibitor domain superfamily / Plant invertase/pectin methylesterase inhibitor / Plant invertase/pectin methylesterase inhibitor / Pectinesterase, Asp active site / Pectinesterase signature 2. / Pectinesterase, catalytic / Pectinesterase / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Pectin lyase fold/virulence factor / 3 Solenoid / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Pectinesterase 1 / Pectinesterase inhibitor
Similarity search - Component
Biological speciesActinidia chinensis (golden kiwifruit)
Solanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsDi Matteo, A. / Raiola, A. / Camardella, L. / Giovane, A. / Bonivento, D. / De Lorenzo, G. / Cervone, F. / Bellincampi, D. / Tsernoglou, D.
Citation
Journal: Plant Cell / Year: 2005
Title: Structural Basis for the Interaction between Pectin Methylesterase and a Specific Inhibitor Protein
Authors: Di Matteo, A. / Giovane, A. / Raiola, A. / Camardella, L. / Bonivento, D. / De Lorenzo, G. / Cervone, F. / Bellincampi, D. / Tsernoglou, D.
#1: Journal: Biochim.Biophys.Acta / Year: 2004
Title: Pectin methylesterase inhibitor
Authors: Giovane, A. / Servillo, L. / Balestrieri, C. / Raiola, A. / D'Avino, R. / Tamburrini, M. / Ciardiello, M.A. / Camardella, L.
#2: Journal: Proteins / Year: 2003
Title: Tomato pectin methylesterase: modeling, fluorescence, and inhibitor interaction studies-comparison with the bacterial (Erwinia chrysanthemi) enzyme
Authors: D'Avino, R. / Camardella, L. / Christensen, T.M. / Giovane, A. / Servillo, L.
#3: Journal: Trends Plant Sci. / Year: 2001
Title: Pectin methylesterases: cell wall enzymes with important roles in plant physiology
Authors: Micheli, F.
History
DepositionSep 16, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pectinesterase 1
B: Pectinesterase inhibitor


Theoretical massNumber of molelcules
Total (without water)51,0242
Polymers51,0242
Non-polymers00
Water8,161453
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.379, 90.379, 149.095
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Pectinesterase 1 / Pectin methylesterase 1 / PE 1


Mass: 34586.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / Tissue: pericarp / References: UniProt: P14280, pectinesterase
#2: Protein Pectinesterase inhibitor / Pectin methylesterase inhibitor / PMEI


Mass: 16438.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinidia chinensis (golden kiwifruit) / Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P83326
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.49 Å3/Da / Density % sol: 64.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: magnesium sulfate, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.99 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 18, 2004 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 56180 / Num. obs: 56180 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.082
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.338 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.902 / SU B: 2.561 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23176 2730 5.1 %RANDOM
Rwork0.19774 ---
all0.19941 51019 --
obs0.19941 51019 95.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.06 Å20 Å2
2--0.13 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3600 0 0 453 4053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223662
X-RAY DIFFRACTIONr_bond_other_d0.0020.023258
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.9494974
X-RAY DIFFRACTIONr_angle_other_deg1.17437607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8695466
X-RAY DIFFRACTIONr_chiral_restr0.0740.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024126
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02719
X-RAY DIFFRACTIONr_nbd_refined0.2080.2742
X-RAY DIFFRACTIONr_nbd_other0.2370.23901
X-RAY DIFFRACTIONr_nbtor_other0.0820.22105
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2328
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3090.227
X-RAY DIFFRACTIONr_mcbond_it0.5921.52320
X-RAY DIFFRACTIONr_mcangle_it1.13823738
X-RAY DIFFRACTIONr_scbond_it1.94731342
X-RAY DIFFRACTIONr_scangle_it3.3774.51236
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.617 148
Rwork0.578 3001

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