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- PDB-7vtl: Crystal structure of GH family 64 beta-1,3-glucanase complexed wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vtl | ||||||
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Title | Crystal structure of GH family 64 beta-1,3-glucanase complexed with Laminaritriose | ||||||
![]() | beta-1,3-glucanase | ||||||
![]() | HYDROLASE / beta-1 / 3-Glucanase / glycoside hydrolase family 64 / carbohydrate binding module | ||||||
Function / homology | 4beta-beta-mannobiose![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jiang, Z.Q. / Ma, J.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of GH family 64 beta-1,3-glucanase complexed with Laminaritriose Authors: Jiang, Z.Q. / Ma, J.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186.6 KB | Display | ![]() |
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PDB format | ![]() | 131.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7vtkS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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
#1: Protein | Mass: 40566.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Polysaccharide | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.83 Å3/Da / Density % sol: 67.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.1M sodium malonate pH 7.0, 0.1M HEPES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jan 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→25.38 Å / Num. obs: 38667 / % possible obs: 97 % / Redundancy: 18.6 % / Biso Wilson estimate: 50.9503395566 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2.07→2.1221 Å / Rmerge(I) obs: 0.079 / Num. unique obs: 38667 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7VTK Resolution: 2.07037904157→25.3769832441 Å / SU ML: 0.232772607368 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.6591252789 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 63.8672822637 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.07037904157→25.3769832441 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 37.2105397521 Å / Origin y: -32.2099839299 Å / Origin z: 14.8690926805 Å
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Refinement TLS group | Selection details: all |