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Yorodumi- PDB-1wp6: Crystal structure of maltohexaose-producing amylase from alkaloph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wp6 | ||||||
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Title | Crystal structure of maltohexaose-producing amylase from alkalophilic Bacillus sp.707. | ||||||
Components | Glucan 1,4-alpha-maltohexaosidase | ||||||
Keywords | HYDROLASE / Alpha-Amylase / Maltohexaose | ||||||
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 space Similarity search - Function | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kanai, R. / Haga, K. / Akiba, T. / Yamane, K. / Harata, K. | ||||||
Citation | 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. #1: Journal: Appl.Microbiol.Biotechnol. / Year: 1988 Title: Cloning of a gene for maltohexaose producing amylase of an alkalophilic Bacillus and hyper-production of the enzyme in Bacillus subtilis cells Authors: Kimura, K. / Tsukamoto, A. / Ishii, Y. / Takano, T. / Yamane, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wp6.cif.gz | 116.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wp6.ent.gz | 88.6 KB | Display | PDB format |
PDBx/mmJSON format | 1wp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wp6_validation.pdf.gz | 446.7 KB | Display | wwPDB validaton report |
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Full document | 1wp6_full_validation.pdf.gz | 449.6 KB | Display | |
Data in XML | 1wp6_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 1wp6_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/1wp6 ftp://data.pdbj.org/pub/pdb/validation_reports/wp/1wp6 | HTTPS FTP |
-Related structure data
Related structure data | 1wpcC 1bvnS 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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-Non-polymers , 5 types, 288 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-PO4 / | #5: Chemical | ChemComp-TRS / | #6: 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: 2.26 Å3/Da / Density % sol: 45.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: MPD, TrisHCl, Ammonium Phosphate, Calcium chloride, Sodium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2003 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→50 Å / Num. all: 33308 / Num. obs: 33010 / % possible obs: 99.6 % / Observed criterion σ(I): 12.8 / Redundancy: 2.6 % / Rmerge(I) obs: 0.091 |
Reflection shell | Resolution: 2.04→2.11 Å / Redundancy: 1.65 % / Rmerge(I) obs: 0.248 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1BVN Resolution: 2.1→6 Å / Isotropic thermal model: Isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→6 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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