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Yorodumi- PDB-1wo2: Crystal structure of the pig pancreatic alpha-amylase complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wo2 | ||||||||||||
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Title | Crystal structure of the pig pancreatic alpha-amylase complexed with malto-oligosaacharides under the effect of the chloride ion | ||||||||||||
Components | Alpha-amylase, pancreatic | ||||||||||||
Keywords | HYDROLASE / BETA-ALPHA-BARRELS | ||||||||||||
Function / homology | Function and homology information alpha-amylase / carbohydrate catabolic process / alpha-amylase activity / chloride ion binding / carbohydrate metabolic process / calcium ion binding / extracellular space Similarity search - Function | ||||||||||||
Biological species | Sus scrofa (pig) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||||||||
Authors | Qian, M. / Payan, F. / Nahoum, V. | ||||||||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Molecular Basis of the Effects of Chloride Ion on the Acid-Base Catalyst in the Mechanism of Pancreatic alpha-Amylase Authors: Qian, M. / Ajandouz, E.H. / Payan, F. / Nahoum, V. #1: Journal: Biochemistry / Year: 2001 Title: Enzyme-catalyzed condensation Reaction in a Mammalian alpha-amylase. High-resolution structural analysis of an enzyme-inhibitor complex Authors: Qian, M. / Nahoum, V. / Bonicel, J. / Bischoff, H. / Henrissat, B. / Payan, F. #2: Journal: J.PROTEIN CHEM. / Year: 2003 Title: Crystal structure of the pig pancreatic alpha-amylase complexed with malto-oligosaccharides Authors: Payan, F. / Qian, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wo2.cif.gz | 127.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wo2.ent.gz | 100.4 KB | Display | PDB format |
PDBx/mmJSON format | 1wo2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/1wo2 ftp://data.pdbj.org/pub/pdb/validation_reports/wo/1wo2 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55472.828 Da / Num. of mol.: 1 / Mutation: Q16PCA Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa / Tissue: PANCREAS / Production host: Escherichia coli (E. coli) / References: UniProt: P00690, alpha-amylase |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | #3: Polysaccharide | alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltose | |
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-Non-polymers , 4 types, 757 molecules
#4: Chemical | ChemComp-CL / | ||
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#5: Chemical | ChemComp-CA / | ||
#6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
-Details
Sequence details | THESE CONFLICTS ARE EXPLAINED IN REFERENCE AS FOLLOWING, M.QIAN,R.HASER,F.PAYAN STRUCTURE AND ...THESE CONFLICTS ARE EXPLAINED IN REFERENCE AS FOLLOWING, M.QIAN,R.HASER,F.PAYAN STRUCTURE AND MOLECULAR MODEL REFINEMENT |
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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: 4.23 Å3/Da / Density % sol: 70 % |
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Crystal grow | Temperature: 277 K / Method: evaporation / pH: 8 Details: Tris, Calcium chloride, Sodium chloride, pH 8, EVAPORATION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 2000 |
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: 2.01→30 Å / Num. all: 62412 / Num. obs: 61363 / % possible obs: 98.32 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.067 |
Reflection shell | Resolution: 2.02→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.173 / Num. unique all: 4603 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→20 Å / Isotropic thermal model: Isotropic / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.01→20 Å
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Refine LS restraints |
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