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Yorodumi- PDB-5h9y: Crystal structure of GH family 64 laminaripentaose-producing beta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h9y | |||||||||
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Title | Crystal structure of GH family 64 laminaripentaose-producing beta-1,3-glucanase from Paenibacillus barengoltzii complexed with laminarihexaose. | |||||||||
Components | beta-1,3-glucanase | |||||||||
Keywords | HYDROLASE / beta-1 / 3-glucan recognition / glycoside hydrolase family 64 / 3-glucanase / GH64-TLP-SF superfamily | |||||||||
Function / homology | Beta-1,3-glucanase, N-terminal, subdomain 2 / Beta-1,3-glucanase, N-terminal / Glucan endo-1,3-beta-glucosidase / Beta-1,3-glucanase / glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / Osmotin/thaumatin-like superfamily / L(+)-TARTARIC ACID / Beta-1,3-glucanase Function and homology information | |||||||||
Biological species | Paenibacillus barengoltzii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.969 Å | |||||||||
Authors | Zhen, Q. / Yan, Q. / Yang, S. / Jiang, Z. / You, X. | |||||||||
Citation | Journal: Chem. Commun. (Camb.) / Year: 2017 Title: The recognition mechanism of triple-helical beta-1,3-glucan by a beta-1,3-glucanase Authors: Qin, Z. / Yang, D. / You, X. / Liu, Y. / Hu, S. / Yan, Q. / Yang, S. / Jiang, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h9y.cif.gz | 113.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h9y.ent.gz | 83.6 KB | Display | PDB format |
PDBx/mmJSON format | 5h9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/5h9y ftp://data.pdbj.org/pub/pdb/validation_reports/h9/5h9y | HTTPS FTP |
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-Related structure data
Related structure data | 5h9xSC 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
#1: Protein | Mass: 49017.820 Da / Num. of mol.: 1 / Mutation: E236A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus barengoltzii (bacteria) / Strain: CAU904 / Plasmid: pET28A Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A1S4NYE2*PLUS, glucan endo-1,3-beta-D-glucosidase |
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#2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D- ...beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Chemical | ChemComp-TLA / |
#5: Water | ChemComp-HOH / |
Sequence details | AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS KU363233 FOR THIS SEQUENCE. The SEQUENCE HAS A ...AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS KU363233 FOR THIS SEQUENCE. The SEQUENCE HAS A MUTATION, E236A. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Se-derivatized PbBgl64A was prepared and concentrated to 15 mg ml-1 in buffer D contain 5 mM DL-Dithiothreitol (DTT), and optimized crystals were grown in drops containing 2 microliter of ...Details: Se-derivatized PbBgl64A was prepared and concentrated to 15 mg ml-1 in buffer D contain 5 mM DL-Dithiothreitol (DTT), and optimized crystals were grown in drops containing 2 microliter of protein solution and 0.5 microliter of reservoir solution (14mM sodium cholate, 1.1M di-Ammonium Tartrate pH 7.0) at 293 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.0093 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0093 Å / Relative weight: 1 |
Reflection | Resolution: 1.969→28.27 Å / Num. obs: 33814 / % possible obs: 93.45 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.09 / Rsym value: 0.042 / Net I/σ(I): 11.21 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.41 / % possible all: 64.54 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H9X Resolution: 1.969→28.27 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.76 / 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: 1.969→28.27 Å
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Refine LS restraints |
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LS refinement shell |
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