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Yorodumi- PDB-7c7d: Crystal structure of the catalytic unit of thermostable GH87 alph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c7d | ||||||
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Title | Crystal structure of the catalytic unit of thermostable GH87 alpha-1,3-glucanase from Streptomyces thermodiastaticus strain HF3-3 | ||||||
Components | alpha-1,3-glucanase | ||||||
Keywords | HYDROLASE / glycosidase | ||||||
Function / homology | Function and homology information CBM6/CBM35/CBM36-like 1 / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Parallel beta-helix repeat / Parallel beta-helix repeats / Coagulation factors 5/8 type C domain (FA58C) profile. / Pectin lyase fold / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Pectin lyase fold/virulence factor ...CBM6/CBM35/CBM36-like 1 / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Parallel beta-helix repeat / Parallel beta-helix repeats / Coagulation factors 5/8 type C domain (FA58C) profile. / Pectin lyase fold / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Pectin lyase fold/virulence factor / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Galactose-binding-like domain superfamily Similarity search - Domain/homology | ||||||
Biological species | Streptomyces thermodiastaticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.16 Å | ||||||
Authors | Itoh, T. / Panti, N. / Toyotake, Y. / Hayashi, J. / Suyotha, W. / Yano, S. / Wakayama, M. / Hibi, T. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: Crystal structure of the catalytic unit of thermostable GH87 alpha-1,3-glucanase from Streptomyces thermodiastaticus strain HF3-3. Authors: Itoh, T. / Panti, N. / Hayashi, J. / Toyotake, Y. / Matsui, D. / Yano, S. / 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 | 7c7d.cif.gz | 460 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c7d.ent.gz | 373.2 KB | Display | PDB format |
PDBx/mmJSON format | 7c7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/7c7d ftp://data.pdbj.org/pub/pdb/validation_reports/c7/7c7d | HTTPS FTP |
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-Related structure data
Related structure data | 5zruS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 63276.133 Da / Num. of mol.: 2 / Fragment: catalytic unit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces thermodiastaticus (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: A0A7G1KW31*PLUS, EC: 3.2.1.59 #2: Chemical | #3: Chemical | ChemComp-1PE / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 1.85 Å3/Da / Density % sol: 33.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 25% (w/v) polyethylene glycol 1500, 0.1 M malonate-imidazole-boric acid buffer, pH 5.0 |
-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: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 22, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→47 Å / Num. obs: 325339 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 11.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.16→1.18 Å / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 15825 / CC1/2: 0.59 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZRU Resolution: 1.16→41.21 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 14.79 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.93 Å2 / Biso mean: 20.9159 Å2 / Biso min: 8.17 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.16→41.21 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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