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Yorodumi- PDB-1hg8: Endopolygalacturonase from the phytopathogenic fungus Fusarium mo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hg8 | |||||||||
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Title | Endopolygalacturonase from the phytopathogenic fungus Fusarium moniliforme | |||||||||
Components | ENDOPOLYGALACTURONASEPolygalacturonase | |||||||||
Keywords | HYDROLASE / PECTIN DEGRADATION | |||||||||
Function / homology | Function and homology information endo-polygalacturonase / polygalacturonase activity / cell wall organization / carbohydrate metabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | FUSARIUM MONILIFORME (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.73 Å | |||||||||
Authors | Federici, L. / Caprari, C. / Mattei, B. / Savino, C. / De Lorenzo, G. / Cervone, F. / Tsernoglou, D. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Structural Requirements of Endopolygalacturonase for the Interaction with Pgip (Polygalacturonase-Inhibiting Protein) Authors: Federici, L. / Caprari, C. / Mattei, B. / Savino, C. / Di Matteo, A. / De Lorenzo, G. / Cervone, F. / Tsernoglou, D. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallization and Preliminary X-Ray Diffraction Study of the Endo-Polygalacturonase from Fusarium Moniliforme. Authors: Federici, L. / Mattei, B. / Caprari, C. / Savino, C. / Cervone, F. / Tsernoglou, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hg8.cif.gz | 82.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hg8.ent.gz | 62.8 KB | Display | PDB format |
PDBx/mmJSON format | 1hg8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/1hg8 ftp://data.pdbj.org/pub/pdb/validation_reports/hg/1hg8 | HTTPS FTP |
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-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: 36222.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) FUSARIUM MONILIFORME (fungus) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q07181 |
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#2: 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 |
#3: Sugar | ChemComp-NAG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 40.9 % | ||||||||||||||||||||||||
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Crystal grow | pH: 4.7 / Details: pH 4.70 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 294 K / Method: vapor diffusion, hanging dropDetails: Federici, L., (2001) Acta Crystallogr.,Sect.D, 55, 1359. pH: 4.7 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→17.9 Å / Num. obs: 37710 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.56 % / Rmerge(I) obs: 0.059 |
Reflection | *PLUS Num. measured all: 204193 |
Reflection shell | *PLUS % possible obs: 96.6 % / Rmerge(I) obs: 0.302 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 1.73→17.9 Å / Cross valid method: FREE R-VALUE / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.73→17.9 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.1728 / Rfactor Rfree: 0.203 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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