+Open data
-Basic information
Entry | Database: PDB / ID: 1bg9 | |||||||||
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Title | BARLEY ALPHA-AMYLASE WITH SUBSTRATE ANALOGUE ACARBOSE | |||||||||
Components | 1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE | |||||||||
Keywords | HYDROLASE / O-GLYCOSYL | |||||||||
Function / homology | Function and homology information starch catabolic process / alpha-amylase / alpha-amylase activity / calcium ion binding Similarity search - Function | |||||||||
Biological species | Hordeum vulgare (barley) | |||||||||
Method | X-RAY DIFFRACTION / REFINEMENT DIFFERENCE FOURIER / Resolution: 2.8 Å | |||||||||
Authors | Kadziola, A. / Haser, R. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Molecular structure of a barley alpha-amylase-inhibitor complex: implications for starch binding and catalysis. Authors: Kadziola, A. / Sogaard, M. / Svensson, B. / Haser, R. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Crystal and Molecular Structure of Barley Alpha-Amylase Authors: Kadziola, A. / Abe, J.I. / Svensson, B. / Haser, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bg9.cif.gz | 99 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bg9.ent.gz | 74.2 KB | Display | PDB format |
PDBx/mmJSON format | 1bg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bg9_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1bg9_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1bg9_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 1bg9_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/1bg9 ftp://data.pdbj.org/pub/pdb/validation_reports/bg/1bg9 | HTTPS FTP |
-Related structure data
Related structure data | 1amyS 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: 44986.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley) / Organ: GERMINATED SEEDS / Variant: CULTIVAR MENUET / References: UniProt: P04063, alpha-amylase | ||||
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#2: Polysaccharide | 4,6-dideoxy-4-{[(1S,5R,6S)-3-formyl-5,6-dihydroxy-4-oxocyclohex-2-en-1-yl]amino}-alpha-D-xylo-hex-5- ...4,6-dideoxy-4-{[(1S,5R,6S)-3-formyl-5,6-dihydroxy-4-oxocyclohex-2-en-1-yl]amino}-alpha-D-xylo-hex-5-enopyranose-(1-4)-beta-D-glucopyranose Type: oligosaccharide / Mass: 477.417 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source | ||||
#3: Chemical | #4: Sugar | ChemComp-AF1 / | #5: 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: 4.67 Å3/Da / Density % sol: 75 % Description: COMPLEX BETWEEN BARLEY ALPHA-AMYLASE AND SUBSTRATE ANALOGUE ACARBOSE | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.7 / Details: pH 6.7 | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 75 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Svensson, B., (1987) J. Biol. Chem., 262, 13682. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Apr 1, 1992 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.729 Å / Num. obs: 17688 / % possible obs: 90.5 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.729→2.9 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.27 / % possible all: 44.8 |
Reflection | *PLUS Num. measured all: 61039 |
Reflection shell | *PLUS % possible obs: 44.8 % |
-Processing
Software |
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Refinement | Method to determine structure: REFINEMENT DIFFERENCE FOURIER Starting model: 1AMY Resolution: 2.8→10 Å Cross valid method: THE VERSION OF X-PLOR (2.1) ORIGINALLY USED FOR REFINEMENT THE FREE R TEST WAS NOT AN OPTION. THEREFORE WE HAVE GIVEN THE OVERALL R FACTOR (TEST+WORKING) INSTEAD OF (WORK) ...Cross valid method: THE VERSION OF X-PLOR (2.1) ORIGINALLY USED FOR REFINEMENT THE FREE R TEST WAS NOT AN OPTION. THEREFORE WE HAVE GIVEN THE OVERALL R FACTOR (TEST+WORKING) INSTEAD OF (WORK) TOGETHER WITH AN ESTIMATE OF THE FREE R (TEST) VALUE BASED ON A SIMULATED ANNEALING REFINEMENT WITH A NEWER VERSION OF X-PLOR (3.1). σ(F): 1
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Displacement parameters | Biso mean: 20.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.92 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 2.1,3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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