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Yorodumi- PDB-1jxk: Role of ethe mobile loop in the mehanism of human salivary amylase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jxk | |||||||||
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Title | Role of ethe mobile loop in the mehanism of human salivary amylase | |||||||||
Components | Alpha-amylase, salivary | |||||||||
Keywords | HYDROLASE / amylase / mutagenesis / catalysis / human / salivary / enzyme / mobile loop | |||||||||
Function / homology | Function and homology information Digestion of dietary carbohydrate / oligosaccharide metabolic process / alpha-amylase / alpha-amylase activity / chloride ion binding / carbohydrate metabolic process / calcium ion binding / extracellular space / extracellular exosome Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Ramasubbu, N. / Ragunath, C. / Wang, Z. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Probing the role of a mobile loop in substrate binding and enzyme activity of human salivary amylase Authors: Ramasubbu, N. / Ragunath, C. / Mishra, P.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jxk.cif.gz | 117.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jxk.ent.gz | 88.9 KB | Display | PDB format |
PDBx/mmJSON format | 1jxk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/1jxk ftp://data.pdbj.org/pub/pdb/validation_reports/jx/1jxk | HTTPS FTP |
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-Related structure data
Related structure data | 1mfuC 1mfvC 1smdS S: Starting model for refinement C: citing same article (ref.) |
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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: 55641.945 Da / Num. of mol.: 1 / Fragment: lacking the loop residues 306-310 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Organ: salivary glands / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P04745, UniProt: P0DTE8*PLUS, alpha-amylase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-CL / |
#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: 2.27 Å3/Da / Density % sol: 45.3 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: MPD, calcium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP at 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 10, 2000 / 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→67.42 Å / Num. all: 39061 / Num. obs: 38401 / % possible obs: 98.31 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 16.857 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.9→1.949 Å / Rmerge(I) obs: 0.057 / Mean I/σ(I) obs: 8.6 / Rsym value: 0.155 / % possible all: 99 |
Reflection | *PLUS Num. measured all: 174537 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SMD Resolution: 1.9→67.42 Å / Cor.coef. Fo:Fc: 0.952 / SU B: 2.8 / SU ML: 0 / SU Rfree: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.1 / Stereochemistry target values: Engh & Huber / Details: MAXIMUM LIKELIHOOD RESTRAINED
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Displacement parameters | Biso mean: 16.857 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→67.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Software | *PLUS Name: REFMAC / Version: 5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.244 / Rfactor Rwork: 0.196 |