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Yorodumi- PDB-6toz: Crystal structure of Bacillus paralicheniformis alpha-amylase in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6toz | ||||||
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Title | Crystal structure of Bacillus paralicheniformis alpha-amylase in complex with acarbose | ||||||
Components | Amylase | ||||||
Keywords | HYDROLASE / amylase / starch binding site | ||||||
Function / homology | Function and homology information alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Bacillus licheniformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.94 Å | ||||||
Authors | Rozeboom, H.J. / Janssen, D.B. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2020 Title: Characterization of the starch surface binding site on Bacillus paralicheniformis alpha-amylase. Authors: Bozic, N. / Rozeboom, H.J. / Loncar, N. / Slavic, M.S. / Janssen, D.B. / Vujcic, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6toz.cif.gz | 217.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6toz.ent.gz | 171.7 KB | Display | PDB format |
PDBx/mmJSON format | 6toz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/6toz ftp://data.pdbj.org/pub/pdb/validation_reports/to/6toz | HTTPS FTP |
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-Related structure data
Related structure data | 6toySC 6tp0C 6tp1C 6tp2C 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: 55313.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: amy / Production host: Escherichia coli (E. coli) / Variant (production host): NEB10beta / References: UniProt: I3P686, alpha-amylase |
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#2: Polysaccharide |
-Non-polymers , 4 types, 475 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3 Å3/Da / Density % sol: 59 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 42-46% Tacsimate, 10 mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→47.01 Å / Num. obs: 49402 / % possible obs: 97.6 % / Redundancy: 9.8 % / Biso Wilson estimate: 12.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.044 / Rrim(I) all: 0.14 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.93→1.97 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.572 / Num. unique obs: 2263 / CC1/2: 0.781 / Rpim(I) all: 0.199 / Rrim(I) all: 0.607 / % possible all: 68 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6TOY Resolution: 1.94→47.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.933 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.111 Details: U VALUES : WITH TLS ADDED 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.77 Å2 / Biso mean: 19.777 Å2 / Biso min: 9.95 Å2
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Refinement step | Cycle: final / Resolution: 1.94→47.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.98 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -8.7 Å / Origin y: -32.28 Å / Origin z: 16.838 Å
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