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Yorodumi- PDB-3bax: N298S Variant of Human Pancreatic Alpha-Amylase in Complex with Azide -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bax | |||||||||
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Title | N298S Variant of Human Pancreatic Alpha-Amylase in Complex with Azide | |||||||||
Components | Pancreatic alpha-amylase | |||||||||
Keywords | HYDROLASE / Amylase / Diabetes / Human / Pancreatic / Enzyme / Catalysis / Anion Activation / Chloride / Azide / Carbohydrate metabolism / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Maurus, R. / Brayer, G.D. | |||||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Alternative catalytic anions differentially modulate human alpha-amylase activity and specificity Authors: Maurus, R. / Begum, A. / Williams, L.K. / Fredriksen, J.R. / Zhang, R. / Withers, S.G. / Brayer, G.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bax.cif.gz | 128.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bax.ent.gz | 95.5 KB | Display | PDB format |
PDBx/mmJSON format | 3bax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/3bax ftp://data.pdbj.org/pub/pdb/validation_reports/ba/3bax | HTTPS FTP |
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-Related structure data
Related structure data | 2qmkC 2qv4C 3baiC 3bajC 3bakC 3bawC 3bayC 1bsiS C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 55904.281 Da / Num. of mol.: 1 / Mutation: N298S 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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#2: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 624 molecules
#3: Chemical | ChemComp-CA / | ||||
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#4: Chemical | ChemComp-CL / | ||||
#5: Chemical | #6: Chemical | #7: 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: 2.06 Å3/Da / Density % sol: 40.16 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 60% 2-methylpentane-2,4-diol, 100 mM cacodylate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / 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→30 Å / Num. all: 36630 / Num. obs: 36630 / Redundancy: 7.1 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 34.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1BSI Resolution: 1.9→30 Å
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Displacement parameters | Biso mean: 19.47 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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