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Yorodumi- PDB-6k0n: Catalytic domain of GH87 alpha-1,3-glucanase in complex with nigerose -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k0n | |||||||||
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Title | Catalytic domain of GH87 alpha-1,3-glucanase in complex with nigerose | |||||||||
Components | Alpha-1,3-glucanase | |||||||||
Keywords | HYDROLASE / GH87 alpha-1 / 3-glucanase / catalytic domain | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Paenibacillus glycanilyticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | |||||||||
Authors | Itoh, T. / Intuy, R. / Suyotha, W. / Hayashi, J. / Yano, S. / Makabe, K. / Wakayama, M. / Hibi, T. | |||||||||
Citation | Journal: Febs J. / Year: 2020 Title: Structural insights into substrate recognition and catalysis by glycoside hydrolase family 87 alpha-1,3-glucanase from Paenibacillus glycanilyticus FH11. Authors: Itoh, T. / Intuy, R. / Suyotha, W. / Hayashi, J. / Yano, S. / Makabe, K. / Wakayama, M. / Hibi, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k0n.cif.gz | 150.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k0n.ent.gz | 111.9 KB | Display | PDB format |
PDBx/mmJSON format | 6k0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/6k0n ftp://data.pdbj.org/pub/pdb/validation_reports/k0/6k0n | HTTPS FTP |
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-Related structure data
Related structure data | 6k0mSC 6k0pC 6k0qC 6k0sC 6k0uC 6k0vC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 4 molecules A
#1: Protein | Mass: 61979.055 Da / Num. of mol.: 1 / Fragment: Catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus glycanilyticus (bacteria) Gene: agl / Production host: Brevibacillus (bacteria) / References: UniProt: A0A068PS59 |
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#2: Polysaccharide |
-Non-polymers , 4 types, 886 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CA / | #5: Chemical | #6: 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: 2.77 Å3/Da / Density % sol: 55.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.5 M (NH4)2SO4, 25% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→46.82 Å / Num. obs: 89788 / % possible obs: 100 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 32.5 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.905 / Num. unique obs: 4456 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6K0M Resolution: 1.6→46.82 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.57
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.25 Å2 / Biso mean: 16.2637 Å2 / Biso min: 5.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→46.82 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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