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Yorodumi- PDB-2iq7: Crystal structure of the polygalacturonase from Colletotrichum lu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iq7 | |||||||||
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Title | Crystal structure of the polygalacturonase from Colletotrichum lupini and its implications for the interaction with polygalacturonase-inhibiting proteins | |||||||||
Components | endopolygalacturonasePolygalacturonase | |||||||||
Keywords | HYDROLASE / parallel beta helix | |||||||||
Function / homology | Function and homology information endo-polygalacturonase / polygalacturonase activity / cell wall organization / carbohydrate metabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | Colletotrichum lupini (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | |||||||||
Authors | Bonivento, D. / Federici, L. / Matteo, A.D. | |||||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins Authors: Bonivento, D. / Pontiggia, D. / Matteo, A.D. / Fernandez-Recio, J. / Salvi, G. / Tsernoglou, D. / Cervone, F. / Lorenzo, G.D. / Federici, L. | |||||||||
History |
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Remark 999 | SEQUENCE AT THE TIME OF PROCESSING, THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE AT THE UNP ...SEQUENCE AT THE TIME OF PROCESSING, THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE AT THE UNP SEQUENCE DATABASE. HOWEVER, THE SEQUENCE HAS BEEN SUBMITTED TO GENEBANK. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iq7.cif.gz | 480.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iq7.ent.gz | 388.4 KB | Display | PDB format |
PDBx/mmJSON format | 2iq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/2iq7 ftp://data.pdbj.org/pub/pdb/validation_reports/iq/2iq7 | HTTPS FTP |
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-Related structure data
Related structure data | 1czfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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7 |
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Unit cell |
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Details | seven monomers are present in the asymmetric unit, each representing a biological unit |
-Components
-Protein , 1 types, 7 molecules ABCDEFG
#1: Protein | Mass: 34213.848 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Colletotrichum lupini (fungus) / References: UniProt: A1E266, endo-polygalacturonase |
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-Sugars , 2 types, 7 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 2448 molecules
#4: Chemical | ChemComp-PG4 / #5: Chemical | #6: Chemical | ChemComp-ACY / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.48 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 24% PEG3000, 0.1M CHES, pH 9.5, 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: 1.2 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2005 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→105.41 Å / Num. all: 165995 / Num. obs: 165995 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.94→2.01 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.396 / Num. unique all: 16003 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1CZF Resolution: 1.94→49.33 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.516 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.138 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.117 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→49.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.993 Å / Total num. of bins used: 20
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