+Open data
-Basic information
Entry | Database: PDB / ID: 1bpl | ||||||
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Title | GLYCOSYLTRANSFERASE | ||||||
Components | (ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE) x 2 | ||||||
Keywords | GLYCOSYLTRANSFERASE / ALPHA-1 / 4-GLUCAN-4-GLUCANOHYDROLASE / ALPHA-AMYLASE GLYCOSYLTRANSFERASE | ||||||
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 / Resolution: 2.2 Å | ||||||
Authors | Machius, M. / Wiegand, G. / Huber, R. | ||||||
Citation | 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 | 1bpl.cif.gz | 110.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bpl.ent.gz | 84.2 KB | Display | PDB format |
PDBx/mmJSON format | 1bpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bpl_validation.pdf.gz | 370.9 KB | Display | wwPDB validaton report |
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Full document | 1bpl_full_validation.pdf.gz | 378.8 KB | Display | |
Data in XML | 1bpl_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 1bpl_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/1bpl ftp://data.pdbj.org/pub/pdb/validation_reports/bp/1bpl | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21807.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus licheniformis (bacteria) / References: UniProt: P06278, alpha-amylase |
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#2: Protein | Mass: 33508.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus licheniformis (bacteria) / References: UniProt: P06278, alpha-amylase |
#3: Water | ChemComp-HOH / |
Compound details | THE CALCIUM FREE FORM OF BLA IS CLEAVED AFTER GLU 189 DUE TO TRACE AMOUNTS OF A GLU-C-ENDOPEPTIDASE ...THE CALCIUM FREE FORM OF BLA IS CLEAVED AFTER GLU 189 DUE TO TRACE AMOUNTS OF A GLU-C-ENDOPEPTID |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 8.2 Details: MOLECULE: ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE FROM BACILLUS LICHENIFORMIS. VAPOR DIFFUSION, ROOM TEMPERATURE PROTEIN SOLUTION: 15 MG/ML BLA IN 0.4 M SODIUM CITRATE 2.5 MM EDTA, PH 8.2 ...Details: MOLECULE: ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE FROM BACILLUS LICHENIFORMIS. VAPOR DIFFUSION, ROOM TEMPERATURE PROTEIN SOLUTION: 15 MG/ML BLA IN 0.4 M SODIUM CITRATE 2.5 MM EDTA, PH 8.2 RESERVOIR: 0.66 M SODIUM CITRATE, 2.5 MM EDTA, PH 8.2 CALCIUM REMOVAL BY EDTA LEADS TO A CLEAVAGE OF BLA AFTER GLU 189 DUE TO TRACE AMOUNTS OF A GLU-C-ENDOPEPTIDASE PRESENT IN THE PREPARATION (SEE PAPER)., vapor diffusion Temp details: room temp | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 9, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.045 |
-Processing
Software |
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Refinement | Resolution: 2.2→8 Å / σ(F): 0 Details: THE CALCIUM FREE FORM OF BLA IS CLEAVED AFTER GLU 189 DUE TO TRACE AMOUNTS OF A GLU-C-ENDOPEPTIDASE PRESENT IN THE PREPARATION. WITHOUT THIS CLEAVAGE, BLA DID NOT CRYSTALLIZE UNDER THE ...Details: THE CALCIUM FREE FORM OF BLA IS CLEAVED AFTER GLU 189 DUE TO TRACE AMOUNTS OF A GLU-C-ENDOPEPTIDASE PRESENT IN THE PREPARATION. WITHOUT THIS CLEAVAGE, BLA DID NOT CRYSTALLIZE UNDER THE CONDITIONS APPLIED. DUE TO THIS CLEAVAGE, THE REGION BETWEEN TRP 182 AND ASN 192 IS NOT VISIBLE IN THE ELECTRON DENSITY. IN ADDITION THE FIRST TWO (N TERMINAL) RESIDUES ALA 1 AND ASN 2 AS WELL AS THE C-TERMINAL ARG 483 ARE NOT VISIBLE. A RAMACHANDRAN PLOT SHOWS THAT TYR 150, WHICH IS WELL DEFINED IN THE DENSITY, IS IN THE DISALLOWED REGION. ARG 134 HAS BEEN MODELED AS LEU AS THIS FITS BETTER INTO THE ELECTRON DENSITY.
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Displacement parameters | Biso mean: 20.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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