+Open data
-Basic information
Entry | Database: PDB / ID: 1jxj | |||||||||
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Title | Role of mobile loop in the mechanism 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: 1.99 Å | |||||||||
Authors | Ramasubbu, N. / Ragunath, C. / Wang, Z. / Mishra, P.J. / Thomas, L.M. | |||||||||
Citation | Journal: Eur.J.Biochem. / Year: 2004 Title: Human salivary alpha-amylase Trp58 situated at subsite -2 is critical for enzyme activity. Authors: Ramasubbu, N. / Ragunath, C. / Mishra, P.J. / Thomas, L.M. / Kandra, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jxj.cif.gz | 117.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jxj.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jxj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/1jxj ftp://data.pdbj.org/pub/pdb/validation_reports/jx/1jxj | HTTPS FTP |
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-Related structure data
Related structure data | 1nm9C 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: 55882.203 Da / Num. of mol.: 1 / Mutation: W58L 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: 2.24 Å3/Da / Density % sol: 44.6 % | ||||||||||||||||||||||||||||||
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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, temperature 298K, temperature 298.0K | ||||||||||||||||||||||||||||||
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 RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 21, 2001 / 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: 1.99→65.94 Å / Num. all: 36288 / Num. obs: 34452 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.051 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.99→2.07 Å / Rmerge(I) obs: 0.062 / Mean I/σ(I) obs: 3 / Rsym value: 0.281 / % possible all: 95 |
Reflection | *PLUS Redundancy: 3.8 % |
Reflection shell | *PLUS % possible obs: 95 % / Rmerge(I) obs: 0.281 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1SMD Resolution: 1.99→65.94 Å / Cor.coef. Fo:Fc: 0.959 / SU B: 3.4 / SU ML: 0 / SU Rfree: 0.1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 22.987 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.99→65.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.995→2.047 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: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.264 / Rfactor Rwork: 0.216 |