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- PDB-6k0u: Catalytic domain of GH87 alpha-1,3-glucanase D1068A in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6k0u | |||||||||
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Title | Catalytic domain of GH87 alpha-1,3-glucanase D1068A in complex with tetrasaccharides | |||||||||
![]() | Alpha-1,3-glucanase | |||||||||
![]() | HYDROLASE / GH87 alpha-1 / 3-glucanase / catalytic domain | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Itoh, T. / Intuy, R. / Suyotha, W. / Hayashi, J. / Yano, S. / Makabe, K. / Wakayama, M. / Hibi, T. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.2 KB | Display | ![]() |
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PDB format | ![]() | 104.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 27 KB | Display | |
Data in CIF | ![]() | 41.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6k0mSC ![]() 6k0nC ![]() 6k0pC ![]() 6k0qC ![]() 6k0sC ![]() 6k0vC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 61935.047 Da / Num. of mol.: 1 / Fragment: Catalytic domain / Mutation: D1068A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: agl / Production host: ![]() |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 558 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.94 % Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.5 M (NH4)2SO4 and 25% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 31, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→42.048 Å / Num. obs: 49682 / % possible obs: 99 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.95→2.07 Å / Rmerge(I) obs: 1.277 / Num. unique obs: 15277 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6K0M Resolution: 1.95→42.048 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.07 Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93 Å2 / Biso mean: 30.3606 Å2 / Biso min: 14.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→42.048 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18
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