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Yorodumi- PDB-6tp2: Crystal structure of Bacillus paralicheniformis alpha-amylase in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tp2 | ||||||
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Title | Crystal structure of Bacillus paralicheniformis alpha-amylase in complex with beta-cyclodextrin | ||||||
Components | Amylase | ||||||
Keywords | HYDROLASE / amylase / starch binding site / cyclodextrin | ||||||
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 | 6tp2.cif.gz | 214.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tp2.ent.gz | 170.2 KB | Display | PDB format |
PDBx/mmJSON format | 6tp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/6tp2 ftp://data.pdbj.org/pub/pdb/validation_reports/tp/6tp2 | HTTPS FTP |
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-Related structure data
Related structure data | 6toySC 6tozC 6tp0C 6tp1C 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, 2 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 | Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin / Cyclodextrin |
-Non-polymers , 4 types, 424 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MLI / | #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: 56 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 41 - 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 17, 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→46.8 Å / Num. obs: 49463 / % possible obs: 98.5 % / Redundancy: 7.6 % / Biso Wilson estimate: 9.7 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.071 / Rrim(I) all: 0.197 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.93→1.97 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.804 / Num. unique obs: 2544 / CC1/2: 0.609 / Rpim(I) all: 0.328 / Rrim(I) all: 0.871 / % possible all: 77.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6TOY Resolution: 1.94→46.8 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.284 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.121 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: 68.14 Å2 / Biso mean: 21.669 Å2 / Biso min: 10.17 Å2
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Refinement step | Cycle: final / Resolution: 1.94→46.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.986 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -8.535 Å / Origin y: -32.206 Å / Origin z: 16.763 Å
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