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- PDB-1mfu: Probing the role of a mobile loop in human salivary amylase: Stru... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mfu | ||||||||||||
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Title | Probing the role of a mobile loop in human salivary amylase: Structural studies on the loop-deleted mutant | ||||||||||||
![]() | alpha-amylase, Salivary![]() | ||||||||||||
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Function / homology | ![]() Digestion of dietary carbohydrate / oligosaccharide metabolic process / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Ramasubbu, N. / Ragunath, C. / Mishra, P.J. | ||||||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.7 KB | Display | ![]() |
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PDB format | ![]() | 94.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1jxkSC ![]() 1mfvC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 55641.945 Da / Num. of mol.: 1 / Mutation: deletion of residues 306 through 310 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P04745, UniProt: P0DTE8*PLUS, ![]() |
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-Sugars , 4 types, 6 molecules ![](data/chem/img/GLC.gif)
#2: Polysaccharide | 4-amino-4,6-dideoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose![]() Source method: isolated from a genetically manipulated source | ||||
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#3: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose | #6: Sugar | ChemComp-GLC / | ![]() |
-Non-polymers , 4 types, 296 molecules ![](data/chem/img/HMC.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-HMC / ![]() #7: Chemical | ChemComp-CA / | #8: Chemical | ChemComp-CL / | ![]() #9: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.53 % |
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Crystal grow![]() | Temperature: 298 K Method: soaking with acarbose at 1 mm concentration for 24 hours pH: 9 Details: 40% mpd, pH 9.0, soaking with acarbose at 1 mM concentration for 24 hours, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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![]() |
Reflection | Resolution: 2→26.54 Å / Num. all: 35031 / Num. obs: 35031 / % possible obs: 96.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 7 / Num. unique all: 3488 / Rsym value: 0.267 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1jxk Resolution: 2→26.54 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: THROUGHOUT / σ(F): 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: 25.789 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→26.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.052 Å / Total num. of bins used: 20 /
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