+Open data
-Basic information
Entry | Database: PDB / ID: 5z3d | ||||||
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Title | Glycosidase F290Y | ||||||
Components | Glycoside hydrolase 15-related protein | ||||||
Keywords | HYDROLASE / Glycosidase | ||||||
Function / homology | Function and homology information isomaltose glucohydrolase / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / cytoplasm Similarity search - Function | ||||||
Biological species | Kribbella flavida DSM 17836 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.25 Å | ||||||
Authors | Tanaka, Y. / Chen, M. / Tagami, T. / Yao, M. / Kimura, A. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Febs J. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z3d.cif.gz | 302 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z3d.ent.gz | 255.3 KB | Display | PDB format |
PDBx/mmJSON format | 5z3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/5z3d ftp://data.pdbj.org/pub/pdb/validation_reports/z3/5z3d | HTTPS FTP |
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-Related structure data
Related structure data | 5z3aC 5z3bC 5z3cC 5z3eC 5z3fC 7c24C 7c25C 7c26C 7c27C C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 44076.055 Da / Num. of mol.: 1 / Mutation: F290Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kribbella flavida DSM 17836 (bacteria) / Strain: DSM 17836 / JCM 10339 / NBRC 14399 / Gene: Kfla_1896 / Production host: Escherichia coli (E. coli) / References: UniProt: D2PPM8 | ||||
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#2: Chemical | #3: Chemical | ChemComp-CIT / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.77 % |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
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: 1.25→45.17 Å / Num. obs: 136955 / % possible obs: 99.8 % / Redundancy: 14.4 % / Net I/σ(I): 25.79 |
Reflection shell | Resolution: 1.25→1.31 Å |
-Processing
Software |
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Refinement | Resolution: 1.25→45.17 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.807 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.028 / 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: 16.81 Å2
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Refinement step | Cycle: 1 / Resolution: 1.25→45.17 Å
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Refine LS restraints |
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