+Open data
-Basic information
Entry | Database: PDB / ID: 1bli | ||||||
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Title | BACILLUS LICHENIFORMIS ALPHA-AMYLASE | ||||||
Components | ALPHA-AMYLASE | ||||||
Keywords | HYDROLASE / GLYCOSYLTRANSFERASE / ALPHA-AMYLASE / STARCH DEGRADATION / ALPHA-1 / 4-GLUCAN-4-GLUCANOHYDROLASE / THERMOSTABILITY / CALCIUM / SODIUM | ||||||
Function / homology | Function and homology information alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / calcium ion binding / extracellular space Similarity search - Function | ||||||
Biological species | Bacillus licheniformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / PATTERSON SEARCH / Resolution: 1.9 Å | ||||||
Authors | Machius, M. / Declerck, N. / Huber, R. / Wiegand, G. | ||||||
Citation | Journal: Structure / Year: 1998 Title: Activation of Bacillus licheniformis alpha-amylase through a disorder-->order transition of the substrate-binding site mediated by a calcium-sodium-calcium metal triad. Authors: Machius, M. / Declerck, N. / Huber, R. / Wiegand, G. #1: Journal: Mol.Cells / Year: 1997 Title: Crystal Structure of Thermostable Alpha-Amylase from Bacillus Licheniformis Refined at 1.7 A Resolution Authors: Hwang, K.Y. / Song, H.K. / Chang, C. / Lee, J. / Lee, S.Y. / Kim, K.K. / Choe, S. / Sweet, R.M. / Suh, S.W. #2: Journal: J.Mol.Biol. / Year: 1995 Title: Crystal Structure of Calcium-Depleted Bacillus Licheniformis Alpha-Amylase at 2.2 A Resolution Authors: Machius, M. / Wiegand, G. / Huber, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bli.cif.gz | 114.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bli.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 1bli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bli_validation.pdf.gz | 367.8 KB | Display | wwPDB validaton report |
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Full document | 1bli_full_validation.pdf.gz | 372.8 KB | Display | |
Data in XML | 1bli_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 1bli_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/1bli ftp://data.pdbj.org/pub/pdb/validation_reports/bl/1bli | HTTPS FTP |
-Related structure data
Related structure data | 1bplS S: Starting model for refinement |
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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
#1: Protein | Mass: 55266.957 Da / Num. of mol.: 1 / Mutation: N190F, Q264S, N265Y Source method: isolated from a genetically manipulated source Details: PROTEIN PRODUCED BY NOVO NORDISK A/S, DENMARK / Source: (gene. exp.) Bacillus licheniformis (bacteria) / Cell line: 293 / Gene: AMYL / Plasmid: PINA9C9 / Cellular location (production host): SECRETED / Production host: Bacillus subtilis (bacteria) / Strain (production host): 293 / References: UniProt: P06278, alpha-amylase | ||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
-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 | pH: 7 / Details: pH 7.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusionDetails: drop consists of equal volume of protein and reservoir solutions | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 278 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1997 / Details: BEAM FOCUSSING MIRROR SYSTEM (MSC, USA) |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→27.5 Å / Num. obs: 46801 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.418 / % possible all: 82.9 |
Reflection shell | *PLUS % possible obs: 82.9 % |
-Processing
Software |
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Refinement | Method to determine structure: PATTERSON SEARCH Starting model: PDB ENTRY 1BPL Resolution: 1.9→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 21.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.23 |