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Yorodumi- PDB-3ij7: Directed 'in situ' Elongation as a Strategy to Characterize the C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ij7 | ||||||||||||
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Title | Directed 'in situ' Elongation as a Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic a-Amylase | ||||||||||||
Components | Pancreatic alpha-amylase | ||||||||||||
Keywords | HYDROLASE / amylase / covalent intermediate / hydrolytic cleavage / catalysis / inhibitor synthesis / enzyme kinetics / human digestion / diabetes / obesity / Carbohydrate metabolism / Chloride / Disulfide bond / Glycoprotein / Glycosidase / Metal-binding / Pyrrolidone carboxylic acid / Secreted | ||||||||||||
Function / homology | Function and homology information polysaccharide digestion / Digestion of dietary carbohydrate / alpha-amylase / carbohydrate catabolic process / alpha-amylase activity / chloride ion binding / carbohydrate metabolic process / calcium ion binding / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Li, C. / Zhang, R. / Withers, S.G. / Brayer, G.D. | ||||||||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Directed "in situ" inhibitor elongation as a strategy to structurally characterize the covalent glycosyl-enzyme intermediate of human pancreatic alpha-amylase Authors: Zhang, R. / Li, C. / Williams, L.K. / Rempel, B.P. / Brayer, G.D. / Withers, S.G. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ij7.cif.gz | 112.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ij7.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ij7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ij7_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3ij7_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3ij7_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 3ij7_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/3ij7 ftp://data.pdbj.org/pub/pdb/validation_reports/ij/3ij7 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | monomer |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55931.305 Da / Num. of mol.: 1 / Fragment: Human Pancreatic alpha-amylase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AMY2A / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P04746, alpha-amylase |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | 4-O-methyl-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-2)-5-fluoro-alpha-L-idopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 4-O-methyl-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranosyl fluoride Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 234 molecules
#4: Chemical | ChemComp-CA / |
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#5: Chemical | ChemComp-CL / |
#6: 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: 2.05 Å3/Da / Density % sol: 40.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 60% 2-methylpentane-2, 4-diol and 100 mM cacodylate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Monochromator: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→28.43 Å / Num. all: 31873 / Num. obs: 30917 / % possible obs: 97 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.07 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.43 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→28.43 Å
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