+
Open data
-
Basic information
Entry | Database: PDB / ID: 7c26 | ||||||
---|---|---|---|---|---|---|---|
Title | Glycosidase Wild Type at pH4.5 | ||||||
![]() | Isomaltose glucohydrolase | ||||||
![]() | HYDROLASE / Glycoside hydrolase | ||||||
Function / homology | ![]() isomaltose glucohydrolase / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tagami, T. / Kikuchi, A. / Okuyama, M. / Kimura, A. | ||||||
![]() | ![]() Title: Structural insights reveal the second base catalyst of isomaltose glucohydrolase. Authors: Tagami, T. / Chen, M. / Furunaga, Y. / Kikuchi, A. / Sadahiro, J. / Lang, W. / Okuyama, M. / Tanaka, Y. / Iwasaki, T. / Yao, M. / Kimura, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 97.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 68.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 465.1 KB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 25.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5z3aSC ![]() 5z3bC ![]() 5z3cC ![]() 5z3dC ![]() 5z3eC ![]() 5z3fC ![]() 7c24C ![]() 7c25C ![]() 7c27C S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 44044.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 17836 / JCM 10339 / NBRC 14399 / Gene: Kfla_1896 / Plasmid: pET28a / Production host: ![]() ![]() | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NH4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.77 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M Ammonium citrate (pH 7.0), 8% PEG monomethyl ether 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.16 Å / Num. obs: 41276 / % possible obs: 87.1 % / Redundancy: 25.8 % / CC1/2: 0.999 / Rrim(I) all: 0.082 / Rsym value: 0.08 / Net I/σ(I): 0.286 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 26.4 % / Mean I/σ(I) obs: 0.023 / Num. unique obs: 6071 / CC1/2: 0.906 / Rrim(I) all: 1.617 / Rsym value: 1.586 / % possible all: 80.6 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5Z3A Resolution: 1.803→47.156 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.572 / SU ML: 0.076 / Cross valid method: FREE R-VALUE / ESU R: 0.116 / ESU R Free: 0.112 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.327 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.803→47.156 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|