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- PDB-5upn: Crystal structure of BhGH81 mutant in complex with laminaro-tetraose -
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Open data
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Basic information
Entry | Database: PDB / ID: 5upn | |||||||||
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Title | Crystal structure of BhGH81 mutant in complex with laminaro-tetraose | |||||||||
![]() | BH0236 protein | |||||||||
![]() | HYDROLASE / (alpha/beta)6 barrel / glycoside hydrolase | |||||||||
Function / homology | ![]() : / endo-1,3(4)-beta-glucanase activity / glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / polysaccharide catabolic process / cell wall organization / carbohydrate binding / cell surface / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Pluvinage, B. / Boraston, A.B. | |||||||||
![]() | ![]() Title: The quaternary structure of beta-1,3-glucan contributes to its recognition and hydrolysis by a multimodular family 81 glycoside hydrolase Authors: Pluvinage, B. / Fillo, A. / Massel, P. / Boraston, A.B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 190.8 KB | Display | ![]() |
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PDB format | ![]() | 146.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 35.3 KB | Display | |
Data in CIF | ![]() | 55.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5upiC ![]() 5upmC ![]() 5upoC ![]() 5v1wC ![]() 5t49S C: citing same article ( S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 85277.633 Da / Num. of mol.: 1 / Fragment: residues 28-779 / Mutation: E542Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125 Gene: BH0236 / Plasmid: pET28a / Production host: ![]() ![]() |
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-Sugars , 4 types, 6 molecules ![](data/chem/img/GLC.gif)
![](data/chem/img/BGC.gif)
![](data/chem/img/BGC.gif)
#2: Polysaccharide | #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: Sugar | ChemComp-GLC / | #5: Sugar | |
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-Non-polymers , 3 types, 824 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-PO4 / #7: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.71 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 15% PEG 10000, 0.2 M ammonium acetate, 0.1 M bis-tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97971 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→79.14 Å / Num. obs: 89565 / % possible obs: 96.7 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.036 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 6 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 5.6 / CC1/2: 0.949 / Rpim(I) all: 0.116 / % possible all: 91.8 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 5T49 Resolution: 1.8→79.14 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.911 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.09 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.96 Å2 / Biso mean: 16.5 Å2 / Biso min: 2.66 Å2
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Refinement step | Cycle: final / Resolution: 1.8→79.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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