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Yorodumi- PDB-6a6c: Crystal structure of carbohydrate-binding module family 56 beta-1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a6c | ||||||
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Title | Crystal structure of carbohydrate-binding module family 56 beta-1,3-glucan binding domain | ||||||
Components | Beta-1,3-glucanase | ||||||
Keywords | SUGAR BINDING PROTEIN / carbohydrate-binding module family 56 / beta-1 / 3-glucan / sugar binding | ||||||
Function / homology | Function and homology information glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity Similarity search - Function | ||||||
Biological species | Paenibacillus barengoltzii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Qin, Z. / Lin, S. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of carbohydrate-binding module family 56 beta-1,3-glucan binding domain Authors: Qin, Z. / Lin, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a6c.cif.gz | 28.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a6c.ent.gz | 17.9 KB | Display | PDB format |
PDBx/mmJSON format | 6a6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/6a6c ftp://data.pdbj.org/pub/pdb/validation_reports/a6/6a6c | HTTPS FTP |
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-Related structure data
Related structure data | 5h9xS 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: 9561.397 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SF file contains Friedel pairs. / Source: (gene. exp.) Paenibacillus barengoltzii (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A1S4NYE1, glucan endo-1,3-beta-D-glucosidase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.8 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 14 mM sodium cholate,1.4 M di-ammonium tartrate, 20 days |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.0093 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0093 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→33.712 Å / Num. obs: 8208 / % possible obs: 87.68 % / Redundancy: 18.5 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 25.86 |
Reflection shell | Resolution: 2.05→2.123 Å / Rmerge(I) obs: 0.412 / Num. unique obs: 537 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H9X Resolution: 2.05→29.472 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→29.472 Å
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Refine LS restraints |
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LS refinement shell |
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