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- PDB-1ib4: Crystal Structure of Polygalacturonase from Aspergillus Aculeatus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ib4 | |||||||||
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Title | Crystal Structure of Polygalacturonase from Aspergillus Aculeatus at Ph4.5 | |||||||||
![]() | POLYGALACTURONASE | |||||||||
![]() | HYDROLASE / POLYGALACTURONASE / GLYCOSYLHYDROLASE | |||||||||
Function / homology | ![]() endo-polygalacturonase / polygalacturonase activity / pectin catabolic process / cell wall organization / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Cho, S.W. / Shin, W. | |||||||||
![]() | ![]() Title: The X-ray structure of Aspergillus aculeatus polygalacturonase and a modeled structure of the polygalacturonase-octagalacturonate complex. Authors: Cho, S.W. / Lee, S. / Shin, W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147.2 KB | Display | ![]() |
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PDB format | ![]() | 118.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 46 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34675.590 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: GenBank: 3220207, UniProt: O74213*PLUS, endo-polygalacturonase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-MAN / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.79 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: microdialysis / pH: 4.6 Details: 30% PEG400, 0.02M CdCl2, 0.1M sodium acetate pH 4.5 , pH 4.6, MICRODIALYSIS, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 4.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: ![]() |
Detector | Type: ENRAF-NONIUS FAST / Detector: AREA DETECTOR / Date: Dec 1, 1999 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. all: 77804 / Num. obs: 33790 / % possible obs: 91.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 2.3 % / Biso Wilson estimate: 3.6 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2→2.13 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.156 / % possible all: 67.3 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 77804 |
Reflection shell | *PLUS Highest resolution: 2.02 Å / % possible obs: 84.6 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Refine analyze | Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5592
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Refinement step | Cycle: LAST / Resolution: 2→24.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å | ||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor Rwork: 0.17 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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