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Yorodumi- PDB-2d3l: Crystal structure of maltohexaose-producing amylase from Bacillus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d3l | |||||||||
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Title | Crystal structure of maltohexaose-producing amylase from Bacillus sp.707 complexed with maltopentaose. | |||||||||
Components | Glucan 1,4-alpha-maltohexaosidase | |||||||||
Keywords | HYDROLASE / Protein-carbohydrate complex / ligand binding | |||||||||
Function / homology | Function and homology information glucan 1,4-alpha-maltohexaosidase / glucan 1,4-alpha-maltohexaosidase activity / starch catabolic process / alpha-amylase activity / calcium ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | Bacillus sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Kanai, R. / Haga, K. / Akiba, T. / Yamane, K. / Harata, K. | |||||||||
Citation | Journal: Protein Sci. / Year: 2006 Title: Role of Trp140 at subsite -6 on the maltohexaose production of maltohexaose-producing amylase from alkalophilic Bacillus sp.707 Authors: Kanai, R. / Haga, K. / Akiba, T. / Yamane, K. / Harata, K. #1: Journal: Biochemistry / Year: 2004 Title: Biochemical and crystallographic analyses of maltohexaose-producing amylase from alkalophilic Bacillus sp. 707 Authors: Kanai, R. / Haga, K. / Akiba, T. / Yamane, K. / Harata, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d3l.cif.gz | 118.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d3l.ent.gz | 90.9 KB | Display | PDB format |
PDBx/mmJSON format | 2d3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/2d3l ftp://data.pdbj.org/pub/pdb/validation_reports/d3/2d3l | HTTPS FTP |
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-Related structure data
Related structure data | 2d3nC 1wp6S 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 , 1 types, 1 molecules A
#1: Protein | Mass: 55438.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: 707 / Plasmid: pTUB812 / Production host: Bacillus subtilis (bacteria) / Strain (production host): 207-25 References: UniProt: P19571, glucan 1,4-alpha-maltohexaosidase |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltopentaose |
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#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose |
#4: Sugar |
-Non-polymers , 3 types, 242 molecules
#5: Chemical | #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
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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: 2.24 Å3/Da / Density % sol: 45.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2,4-dimethylpentanediol, Tris-HCl, Ammonium Phosphate, Calcium chloride, Sodium chloride, Maltopentaose, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1.15 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 7, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.15 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→20 Å / Num. obs: 31896 / % possible obs: 97.8 % / Redundancy: 2.3 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.168 |
Reflection shell | Resolution: 2.06→2.13 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.346 / Num. unique all: 2692 / % possible all: 86.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Native structure (1WP6) Resolution: 2.3→6 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 169554.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.3378 Å2 / ksol: 0.622051 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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