+Open data
-Basic information
Entry | Database: PDB / ID: 5x3i | ||||||
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Title | Kfla1895 D451A mutant | ||||||
Components | Glycoside hydrolase family 31 | ||||||
Keywords | HYDROLASE / glycoside hydrolase TIM-barrel | ||||||
Function / homology | Function and homology information 1,3-alpha-isomaltosidase / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Kribbella flavida DSM 17836 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Tanaka, Y. / Chen, M. / Tagami, T. / Yao, M. / Kimura, A. | ||||||
Citation | Journal: To Be Published Title: Glycoside hydrolase mutant Authors: Tanaka, Y. / Chen, M. / Tagami, 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 | 5x3i.cif.gz | 307 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x3i.ent.gz | 246.2 KB | Display | PDB format |
PDBx/mmJSON format | 5x3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/5x3i ftp://data.pdbj.org/pub/pdb/validation_reports/x3/5x3i | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 82316.641 Da / Num. of mol.: 2 / Mutation: D451A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kribbella flavida DSM 17836 (bacteria) / Strain: DSM 17836 / Gene: Kfla_1895 / Production host: Escherichia coli (E. coli) / References: UniProt: D2PPM7 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.76 Å3/Da / Density % sol: 67.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 0.8 M lithium sulfate, 0.1 M imidazole |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48.55 Å / Num. obs: 143534 / % possible obs: 100 % / Redundancy: 20.5 % / Net I/σ(I): 22.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48.546 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→48.546 Å
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Refine LS restraints |
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LS refinement shell |
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