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Open data
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Basic information
Entry | Database: PDB / ID: 5z3f | |||||||||
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Title | Glycosidase E335A in complex with glucose | |||||||||
![]() | 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 | ![]() | 305.1 KB | Display | ![]() |
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PDB format | ![]() | 248.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.4 KB | Display | ![]() |
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Full document | ![]() | 479.9 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 31.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5z3aC ![]() 5z3bC ![]() 5z3cC ![]() 5z3dC ![]() 5z3eC ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 43970.023 Da / Num. of mol.: 1 / Mutation: E335A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 17836 / JCM 10339 / NBRC 14399 / Gene: Kfla_1896 / Production host: ![]() ![]() | ||||
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#2: Sugar | ChemComp-BGC / | ||||
#3: Chemical | #4: Chemical | ChemComp-CIT / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.99 % |
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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% PEGmonomethyl ether 2000, 2mM isomaltose |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→46.88 Å / Num. obs: 200183 / % possible obs: 99.9 % / Redundancy: 18.8 % / Net I/σ(I): 16.39 |
Reflection shell | Resolution: 1.1→1.16 Å |
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Processing
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Refinement | Resolution: 1.1→46.88 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.457 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.669 Å2
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Refinement step | Cycle: 1 / Resolution: 1.1→46.88 Å
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Refine LS restraints |
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