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Yorodumi- PDB-1vah: Crystal structure of the pig pancreatic-amylase complexed with r-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vah | ||||||
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Title | Crystal structure of the pig pancreatic-amylase complexed with r-nitrophenyl-a-D-maltoside | ||||||
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: 2.4 Å | ||||||
Authors | Zhuo, H. / Payan, F. / Qian, M. | ||||||
Citation | Journal: Protein J. / Year: 2004 Title: Crystal structure of the pig pancreatic alpha-amylase complexed with rho-nitrophenyl-alpha-D-maltoside-flexibility in the active site Authors: Zhuo, H. / 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. #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 | 1vah.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vah.ent.gz | 86.2 KB | Display | PDB format |
PDBx/mmJSON format | 1vah.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/1vah ftp://data.pdbj.org/pub/pdb/validation_reports/va/1vah | 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
#1: Protein | Mass: 55474.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00690, alpha-amylase |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-NPO / |
#5: 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: 2.23 Å3/Da / Density % sol: 44.48 % |
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Crystal grow | Temperature: 295 K / Method: liquid diffusion / pH: 8 Details: SODIUM CHLORIDE, CALSIUM CHLORIDE, pH 8.0, LIQUID DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 25, 1993 |
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: 2.17→44.55 Å / Num. all: 67918 / Num. obs: 25889 / % possible obs: 85 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.055 |
Reflection shell | Resolution: 2.4→2.44 Å / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→35 Å / Isotropic thermal model: Isotropic / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→35 Å
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Refine LS restraints |
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