+Open data
-Basic information
Entry | Database: PDB / ID: 1b1y | |||||||||
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Title | SEVENFOLD MUTANT OF BARLEY BETA-AMYLASE | |||||||||
Components | PROTEIN (BETA-AMYLASE) | |||||||||
Keywords | HYDROLASE / HYDROLASE(O-GLYCOSYL) | |||||||||
Function / homology | Function and homology information beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / polysaccharide catabolic process / identical protein binding Similarity search - Function | |||||||||
Biological species | Hordeum vulgare (barley) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Mikami, B. / Yoon, H.J. / Yoshigi, N. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: The crystal structure of the sevenfold mutant of barley beta-amylase with increased thermostability at 2.5 A resolution. Authors: Mikami, B. / Yoon, H.J. / Yoshigi, N. #1: Journal: J.Biochem.(Tokyo) / Year: 1995 Title: Construction of a Plasmid Used for the Expression of a Sevenfold-Mutant Barley Beta-Amylase with Increased Thermostability in Escherichia Coli and Properties of the Sevenfold-Mutant Beta-Amylase Authors: Yoshigi, N. / Okada, Y. / Maeba, H. / Sahara, H. / Tamaki, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b1y.cif.gz | 116.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b1y.ent.gz | 88.5 KB | Display | PDB format |
PDBx/mmJSON format | 1b1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/1b1y ftp://data.pdbj.org/pub/pdb/validation_reports/b1/1b1y | HTTPS FTP |
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-Related structure data
Related structure data | 1btcS 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: 56317.328 Da / Num. of mol.: 1 / Mutation: M185L,S295A,I297V,S350P,S351P,Q352D,A376S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hordeum vulgare (barley) / Variant: CV. HARUNA / Plasmid: PB927 / Production host: Escherichia coli (E. coli) / Variant (production host): JM 109 / References: UniProt: P16098, beta-amylase |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltose |
#3: Sugar | ChemComp-BGC / |
#4: Water | ChemComp-HOH / |
Sequence details | REF.2 AND REF.3 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 57.43 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.1 Details: HUNGING DROP VAPOR DIFFUSION AGAINST 0.1 M PIPES PH 7.1, 0.1 M MGAC2 AND 14% PEG 6000 WITH A PROTEIN CONCENTRATION OF 3 MG/ML., vapor diffusion - hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Apr 1, 1996 |
Radiation | Monochromator: CARBON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 22631 / % possible obs: 94.3 % / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Rsym value: 0.086 |
Reflection | *PLUS Num. measured all: 122221 / Rmerge(I) obs: 0.086 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BTC Resolution: 2.5→10 Å / σ(F): 2
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Displacement parameters | Biso mean: 31.14 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 10 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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