[English] 日本語
Yorodumi- PDB-2e8z: Crystal structure of pullulanase type I from Bacillus subtilis st... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e8z | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of pullulanase type I from Bacillus subtilis str. 168 complexed with alpha-cyclodextrin | |||||||||
Components | AmyX protein | |||||||||
Keywords | HYDROLASE / multiple domain / beta-alpha-barrel / alpha-amylase-family / alpha-cyclodextrin | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Mikami, B. / Malle, D. / Utsumi, S. / Iwamoto, H. / Katsuya, Y. | |||||||||
Citation | Journal: To be Published Title: Crystal structure of pullulanase type I from Bacillus subtilis str. 168 in complex with maltose and alpha-cyclodextrin Authors: Malle, D. / Iwamoto, H. / Katsuya, Y. / Utsumi, S. / Mikami, B. #1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2006 Title: Overexpression, purification and preliminary X-ray analysis of pullulanase from Bacillus subtilis strain 168 Authors: Malle, D. / Itoh, T. / Hashimoto, W. / Murata, K. / Utsumi, S. / Mikami, B. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2e8z.cif.gz | 306.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2e8z.ent.gz | 246.4 KB | Display | PDB format |
PDBx/mmJSON format | 2e8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/2e8z ftp://data.pdbj.org/pub/pdb/validation_reports/e8/2e8z | HTTPS FTP |
---|
-Related structure data
Related structure data | 2e8yC 2e9bC 2fgzS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 81206.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: amyX / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): HMS 174 References: UniProt: O34587, UniProt: C0SPA0*PLUS, pullulanase #2: Polysaccharide | |
---|
-Non-polymers , 4 types, 673 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.2 Details: 10% PEG 4000, 0.1M sodium acetate buffer, 0.2M magnesium acetate, 20mM alpha-cyclodextrin, pH 5.2, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 16, 2005 / Details: mirrors |
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: 2.2→40 Å / Num. all: 87567 / Num. obs: 87392 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.424 / Num. unique all: 8610 / % possible all: 99.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FGZ Resolution: 2.2→14.97 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3696398.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.5008 Å2 / ksol: 0.380901 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→14.97 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|