[English] 日本語
Yorodumi- PDB-1wpc: Crystal structure of maltohexaose-producing amylase complexed wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wpc | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of maltohexaose-producing amylase complexed with pseudo-maltononaose | |||||||||
Components | Glucan 1,4-alpha-maltohexaosidase | |||||||||
Keywords | HYDROLASE / Maltohexaose-producing amylase / alpha-amylase / acarbose | |||||||||
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: 1.9 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1wpc.cif.gz | 123.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1wpc.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 1wpc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wpc_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1wpc_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1wpc_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 1wpc_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/1wpc ftp://data.pdbj.org/pub/pdb/validation_reports/wp/1wpc | HTTPS FTP |
-Related structure data
Related structure data | 1wp6SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|
-Sugars , 3 types, 4 molecules
#2: Polysaccharide | 4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)- ...4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#3: Polysaccharide | 4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide |
-Non-polymers , 4 types, 330 molecules
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.4 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: MPD, TrisHCl, Ammonium Phosphate, Calcium Chloride, Sodium Chloride, Acarbose, Maltotriose, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 3, 2003 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 39906 / Num. obs: 39475 / % possible obs: 98.8 % / Observed criterion σ(I): 27.9 / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.053 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 0.106 / % possible all: 98.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WP6 Resolution: 1.9→6 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 834402.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 93.1978 Å2 / ksol: 0.713919 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|