+Open data
-Basic information
Entry | Database: PDB / ID: 6j0t | |||||||||
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Title | The crystal structure of exoinulinase INU1 | |||||||||
Components | Inulinase | |||||||||
Keywords | HYDROLASE / Exoinulinase / GH32 | |||||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Kluyveromyces marxianus DMKU3-1042 (yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Hu, X.-J. | |||||||||
Citation | Journal: To Be Published Title: The Crystal Structure Study of Exoinulinase INU1 Authors: Li, L. / Su, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j0t.cif.gz | 213.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j0t.ent.gz | 170 KB | Display | PDB format |
PDBx/mmJSON format | 6j0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/6j0t ftp://data.pdbj.org/pub/pdb/validation_reports/j0/6j0t | HTTPS FTP |
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-Related structure data
Related structure data | 4eqvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 62343.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces marxianus DMKU3-1042 (yeast) Strain: DMKU3-1042 / Gene: INU1 / Production host: Komagataella pastoris (fungus) / References: UniProt: W0T408 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-MG / | #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: 2.58 Å3/Da / Density % sol: 52.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 18% PEG4000, 0.1 M sodium cacodylate pH6.0, 0.2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.00822 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jun 17, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00822 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→49.84 Å / Num. obs: 32347 / % possible obs: 99.86 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 3 / Num. unique obs: 3177 / % possible all: 99.94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EQV Resolution: 2.8→49.84 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→49.84 Å
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Refine LS restraints |
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LS refinement shell |
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