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Open data
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Basic information
Entry | Database: PDB / ID: 5z3a | ||||||
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Title | Glycosidase Wild Type | ||||||
![]() | Glycoside hydrolase 15-related protein | ||||||
![]() | HYDROLASE / Glycosidase | ||||||
Function / homology | ![]() isomaltose glucohydrolase / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tanaka, Y. / Chen, M. / Tagami, T. / Yao, M. / Kimura, A. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 234.9 KB | Display | ![]() |
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PDB format | ![]() | 191.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.2 KB | Display | ![]() |
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Full document | ![]() | 444.7 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 27.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5z3bC ![]() 5z3cC ![]() 5z3dC ![]() 5z3eC ![]() 5z3fC ![]() 7c24C ![]() 7c25C ![]() 7c26C ![]() 7c27C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 44028.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-CIT / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2M Ammonium citrate tribasic (pH 6.8), 0.1M Sodium citrate (pH 5.5), 12% PEG monomethyl ether 2000, 2mM glucose |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→89.49 Å / Num. obs: 97738 / % possible obs: 99.9 % / Redundancy: 14.4 % / Net I/σ(I): 26.69 |
Reflection shell | Resolution: 1.4→1.48 Å |
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Processing
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Refinement | Resolution: 1.401→46.842 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 11.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.401→46.842 Å
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Refine LS restraints |
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LS refinement shell |
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