+Open data
-Basic information
Entry | Database: PDB / ID: 3blk | ||||||||||||
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Title | Role of aromatic residues in starch binding | ||||||||||||
Components | Alpha-amylase 1AMY1A | ||||||||||||
Keywords | HYDROLASE / TIM Barrel / Greek Key barrel / Calcium / Carbohydrate metabolism / Chloride / Glycoprotein / Glycosidase / Metal-binding / Pyrrolidone carboxylic acid / Secreted | ||||||||||||
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. | ||||||||||||
Citation | Journal: Biologia / Year: 2008 Title: Structure-function relationships in human salivary alpha-amylase: role of aromatic residues in a secondary binding site Authors: Ragunath, C. / Manuel, S.G.A. / Kasinathan, C. / Ramasubbu, N. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3blk.cif.gz | 118 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3blk.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 3blk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/3blk ftp://data.pdbj.org/pub/pdb/validation_reports/bl/3blk | HTTPS FTP |
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-Related structure data
Related structure data | 3blpC 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 / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 55840.125 Da / Num. of mol.: 1 / Mutation: W316A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AMY1A, AMY1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P04745, UniProt: P0DTE8*PLUS, alpha-amylase |
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 191 molecules
#3: Chemical | ChemComp-CA / |
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#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-HMC / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 45% MPD, 0.1M Tris.HCl, 10 mM calcium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9777 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 18, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9777 Å / Relative weight: 1 |
Reflection | Resolution: 2→36.16 Å / Num. all: 36537 / Num. obs: 34563 / % possible obs: 99.08 % / Observed criterion σ(F): 1 / Redundancy: 5.4 % / Biso Wilson estimate: 40.9 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 34.2 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 7.6 / Num. unique all: 1810 / Rsym value: 0.418 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SMD Resolution: 2→36.16 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.664 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.573 Å2
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Refine analyze | Luzzati coordinate error obs: 0.071 Å / Luzzati sigma a obs: 0.219 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→36.16 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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