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Yorodumi- PDB-1mfv: Probing the role of a mobile loop in human slaivary amylase: Stru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mfv | ||||||||||||
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Title | Probing the role of a mobile loop in human slaivary amylase: Structural studies on the loop-deleted enzyme | ||||||||||||
Components | alpha-amylase, salivary | ||||||||||||
Keywords | HYDROLASE / amylase / mutagenesis / acarbose / inhibitor | ||||||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Ramasubbu, N. / Ragunath, C. / Mishra, P.J. | ||||||||||||
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 | 1mfv.cif.gz | 114.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mfv.ent.gz | 90.9 KB | Display | PDB format |
PDBx/mmJSON format | 1mfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mfv_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1mfv_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 1mfv_validation.xml.gz | 22 KB | Display | |
Data in CIF | 1mfv_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/1mfv ftp://data.pdbj.org/pub/pdb/validation_reports/mf/1mfv | HTTPS FTP |
-Related structure data
Related structure data | 1jxkC 1mfuC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55955.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVL1392 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P04745, UniProt: P0DTE8*PLUS, alpha-amylase |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 4-amino-4,6-dideoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 247 molecules
#4: Chemical | #5: Chemical | ChemComp-CA / | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-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: 45.85 % |
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Crystal grow | Temperature: 298 K Method: vapordiffusion, combined with soaking with inhibitor at 1 mm concentration pH: 9 Details: 40% MPD, pH 9.0, vapordiffusion, combined with soaking with inhibitor at 1 mM concentration, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 31, 2002 / Details: monochromator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 34179 / Num. obs: 34179 / % possible obs: 96.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 32 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 5.8 / Rsym value: 0.37 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb code 1smd Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.086 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20 /
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