[English] 日本語
Yorodumi- PDB-1ua3: Crystal structure of the pig pancreatic a-amylase complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ua3 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the pig pancreatic a-amylase complexed with malto-oligosaccharides | |||||||||
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 | Payan, F. / Qian, M. | |||||||||
Citation | Journal: J.PROTEIN CHEM. / Year: 2003 Title: Crystal Structure of the Pig Pancreatic alpha-Amylase Complexed with Malto-Oligosaccharides Authors: Payan, F. / Qian, M. #1: Journal: PROTEIN SCI. / Year: 1997 Title: Structure of a pancreatic alpha-amylase bound to a substrate analogue at 2.03 A resolution Authors: Qian, M. / Spinelli, S. / Driguez, H. / Payan, F. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ua3.cif.gz | 131.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ua3.ent.gz | 100.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ua3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/1ua3 ftp://data.pdbj.org/pub/pdb/validation_reports/ua/1ua3 | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55489.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00690, alpha-amylase |
---|
-Sugars , 3 types, 4 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose | ||
---|---|---|---|
#3: Polysaccharide | #6: Sugar | ChemComp-BGC / | |
-Non-polymers , 4 types, 768 molecules
#4: Chemical | #5: Chemical | ChemComp-CA / | #7: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 63.71 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: liquid diffusion / pH: 8 Details: Sodium chloride, Calsium chloride, pH 8.0, LIQUID DIFFUSION, temperature 277K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop / Details: White, J.L., (1982) FEBS Lett., 148, 87. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 20, 1996 |
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: 62336 / Num. obs: 61298 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.01→2.04 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 1.6 / % possible all: 85.8 |
Reflection | *PLUS Lowest resolution: 35 Å / Num. obs: 61415 / Num. measured all: 211556 |
Reflection shell | *PLUS % possible obs: 85.8 % |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→30 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→30 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 35 Å / Rfactor Rfree: 0.198 / Rfactor Rwork: 0.1701 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.01 Å / Lowest resolution: 2.08 Å / Rfactor Rfree: 0.2349 / Rfactor Rwork: 0.2182 |