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Yorodumi- PDB-1kbb: Mechanistic Analyses of Catalysis in Human Pancreatic alpha-Amyla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kbb | |||||||||
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Title | Mechanistic Analyses of Catalysis in Human Pancreatic alpha-Amylase: Detailed Kinetic and Structural Studies of Mutants of Three Conserved Carboxylic Acids | |||||||||
Components | ALPHA-AMYLASE, PANCREATIC | |||||||||
Keywords | HYDROLASE / Amylase / Glycosylation / Mutagenesis / Diabetes / Glycosidase / Carbohydrate metabolism / Catalysis / Pancreatic / enzyme / Human | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Rydberg, E.H. / Li, C. / Maurus, R. / Overall, C.M. / Brayer, G.D. / Withers, S.G. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Mechanistic analyses of catalysis in human pancreatic alpha-amylase: detailed kinetic and structural studies of mutants of three conserved carboxylic acids. Authors: Rydberg, E.H. / Li, C. / Maurus, R. / Overall, C.M. / 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 | 1kbb.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kbb.ent.gz | 87.4 KB | Display | PDB format |
PDBx/mmJSON format | 1kbb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/1kbb ftp://data.pdbj.org/pub/pdb/validation_reports/kb/1kbb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 55873.270 Da / Num. of mol.: 1 / Mutation: E233A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: P04746, alpha-amylase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-CL / |
#4: 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: 2.42 Å3/Da / Density % sol: 49.25 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MPD, cacodylate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS Details: Brayer, G.D., (2000) Biochemistry, 39, 4778. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 2, 1999 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→10 Å / Num. all: 43967 / Num. obs: 40335 / % possible obs: 92.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.058 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.3 / Num. unique all: 3492 / % possible all: 80.9 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 10 Å / Redundancy: 5.8 % / Num. measured all: 234194 / Rmerge(I) obs: 0.05 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor obs: 0.161 / Rfactor Rfree: 0.196 / Rfactor Rwork: 0.161 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS
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