[English] 日本語
Yorodumi- PDB-1wmr: Crystal Structure of Isopullulanase from Aspergillus niger ATCC 9642 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wmr | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of Isopullulanase from Aspergillus niger ATCC 9642 | |||||||||
Components | Isopullulanase | |||||||||
Keywords | HYDROLASE / pullulan / glycoside hydrolase family 49 / glycoprotein | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Aspergillus niger (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Mizuno, M. / Tonozuka, T. / Miyasaka, Y. / Akeboshi, H. / Kamitori, S. / Nishikawa, A. / Sakano, Y. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Crystal Structure of Aspergillus niger Isopullulanase, a Member of Glycoside Hydrolase Family 49 Authors: Mizuno, M. / Koide, A. / Yamamura, A. / Akeboshi, H. / Yoshida, H. / Kamitori, S. / Sakano, Y. / Nishikawa, A. / Tonozuka, T. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1wmr.cif.gz | 236.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1wmr.ent.gz | 190.2 KB | Display | PDB format |
PDBx/mmJSON format | 1wmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wmr_validation.pdf.gz | 478.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1wmr_full_validation.pdf.gz | 509.7 KB | Display | |
Data in XML | 1wmr_validation.xml.gz | 49.7 KB | Display | |
Data in CIF | 1wmr_validation.cif.gz | 71.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/1wmr ftp://data.pdbj.org/pub/pdb/validation_reports/wm/1wmr | HTTPS FTP |
-Related structure data
Related structure data | 1x0cC 2z8gC 1ogmS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 60038.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus niger (mold) / Production host: Pichia pastoris (fungus) / References: UniProt: O00105, isopullulanase #2: Sugar | ChemComp-NAG / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47.4 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: PEG8000, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 45256 / Num. obs: 45256 / % possible obs: 99.9 % / Biso Wilson estimate: 20.8 Å2 |
Reflection shell | Resolution: 2.4→2.49 Å / % possible all: 99 |
-Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OGM Resolution: 2.4→49.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2580600.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.2284 Å2 / ksol: 0.357607 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→49.76 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|