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Yorodumi- PDB-1kgx: Three Dimensional Structure Analysis of the R195Q Variant of Huma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kgx | |||||||||
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Title | Three Dimensional Structure Analysis of the R195Q Variant of Human Pancreatic Alpha Amylase | |||||||||
Components | ALPHA-AMYLASE, PANCREATIC | |||||||||
Keywords | HYDROLASE / ALPHA-AMYLASE / CHLORIDE BINDING / PICHIA PASTORIS / MUTAGENESIS / 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: 2 Å | |||||||||
Authors | Numao, S. / Maurus, R. / Sidhu, G. / Wang, Y. / Overall, C.M. / Brayer, G.D. / Withers, S.G. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Probing the role of the chloride ion in the mechanism of human pancreatic alpha-amylase. Authors: Numao, S. / Maurus, R. / Sidhu, G. / Wang, Y. / 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 | 1kgx.cif.gz | 117.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kgx.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 1kgx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/1kgx ftp://data.pdbj.org/pub/pdb/validation_reports/kg/1kgx | HTTPS FTP |
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-Related structure data
Related structure data | 1kb3C 1kguC 1kgwC 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
#1: Protein | Mass: 55902.238 Da / Num. of mol.: 1 / Mutation: R195Q 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: Sugar | ChemComp-NAG / |
#3: Chemical | ChemComp-CA / |
#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: 2.16 Å3/Da / Density % sol: 43.03 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / 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: Jul 9, 1999 / Details: mirrors |
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 32187 / Num. obs: 32187 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.093 / Mean I/σ(I) obs: 10.7 / % possible all: 73 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 88 % / Num. measured all: 312384 |
Reflection shell | *PLUS Highest resolution: 2 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BSI Resolution: 2→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 22.6 Å2 | ||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 10 Å / σ(F): 0 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.6 Å2 | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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