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- PDB-1kbk: Mechanistic Analyses of Catalysis in Human Pancreatic Alpha-Amyla... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kbk | |||||||||
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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 | |||||||||
![]() | ALPHA-AMYLASE, PANCREATIC | |||||||||
![]() | HYDROLASE / Amylase / Glycosylation / Mutagenesis / Diabetes / Glycosidase / Carbohydrate metabolism / Catalysis / Pancreatic / enzyme / Human | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Rydberg, E.H. / Li, C. / Maurus, R. / Overall, C.M. / Brayer, G.D. / Withers, S.G. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.2 KB | Display | ![]() |
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PDB format | ![]() | 87.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.1 KB | Display | ![]() |
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Full document | ![]() | 448.8 KB | Display | |
Data in XML | ![]() | 20.8 KB | Display | |
Data in CIF | ![]() | 29.1 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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Unit cell |
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Components
#1: Protein | Mass: 55887.293 Da / Num. of mol.: 1 / Mutation: D197A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Sugar | ChemComp-NAG / |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.14 % | ||||||||||||||||||||
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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: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 27, 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: 38711 / Num. obs: 34783 / % possible obs: 89.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.069 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 89.2 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. measured all: 218502 |
Reflection shell | *PLUS Redundancy: 3.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 0.165 / Rfactor Rfree: 0.204 / Rfactor Rwork: 0.165 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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