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Yorodumi- PDB-1xg2: Crystal structure of the complex between pectin methylesterase an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xg2 | ||||||
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Title | Crystal structure of the complex between pectin methylesterase and its inhibitor protein | ||||||
Components |
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Keywords | HYDROLASE/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 / cell wall / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Actinidia chinensis (golden kiwifruit) Solanum lycopersicum (tomato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å | ||||||
Authors | Di 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xg2.cif.gz | 107.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xg2.ent.gz | 86.8 KB | Display | PDB format |
PDBx/mmJSON format | 1xg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xg2_validation.pdf.gz | 428.3 KB | Display | wwPDB validaton report |
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Full document | 1xg2_full_validation.pdf.gz | 430.7 KB | Display | |
Data in XML | 1xg2_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 1xg2_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/1xg2 ftp://data.pdbj.org/pub/pdb/validation_reports/xg/1xg2 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Protein | 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.46 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 Details: magnesium sulfate, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.99 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 18, 2004 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.338 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.18 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.95 Å / Total num. of bins used: 20 /
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