+Open data
-Basic information
Entry | Database: PDB / ID: 5zru | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Agl-KA catalytic domain | ||||||
Components | Alpha-1,3-glucanase | ||||||
Keywords | HYDROLASE / Agl-KA GH87 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus circulans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.833 Å | ||||||
Authors | Yano, S. / Makabe, K. | ||||||
Citation | Journal: Sci Rep / Year: 2019 Title: Crystal structure of the catalytic unit of GH 87-type alpha-1,3-glucanase Agl-KA from Bacillus circulans. Authors: Yano, S. / Suyotha, W. / Oguro, N. / Matsui, T. / Shiga, S. / Itoh, T. / Hibi, T. / Tanaka, Y. / Wakayama, M. / Makabe, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5zru.cif.gz | 261.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5zru.ent.gz | 203.7 KB | Display | PDB format |
PDBx/mmJSON format | 5zru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zru_validation.pdf.gz | 866.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5zru_full_validation.pdf.gz | 871.7 KB | Display | |
Data in XML | 5zru_validation.xml.gz | 50.9 KB | Display | |
Data in CIF | 5zru_validation.cif.gz | 77.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/5zru ftp://data.pdbj.org/pub/pdb/validation_reports/zr/5zru | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AC
#1: Protein | Mass: 62249.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus circulans (bacteria) / Gene: agl / Production host: Escherichia coli (E. coli) / References: UniProt: Q0WYG9 |
---|
-Non-polymers , 5 types, 1160 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.15 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 10% PEG 6000, 0.1M HEPES(pH8.5), 10mM ZnSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→20 Å / Num. obs: 98671 / % possible obs: 99.4 % / Redundancy: 3.4 % / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.83→1.86 Å |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.833→19.947 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.29
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.833→19.947 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|