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Open data
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Basic information
Entry | Database: PDB / ID: 8ip1 | ||||||
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Title | Escherichia coli OpgD mutant-D388N with beta-1,2-glucan | ||||||
![]() | Glucans biosynthesis protein D | ||||||
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Function / homology | ![]() beta-glucan biosynthetic process / glucan biosynthetic process / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Motouchi, S. / Nakajima, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Novel glycoside hydrolase family enzymes from Escherichia coli associating with osmo-regulated periplasmic glucan synthesis Authors: Motouchi, S. / Nakajima, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 232.5 KB | Display | ![]() |
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PDB format | ![]() | 183.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8ioxC ![]() 8ip2C C: citing same article ( |
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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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 63899.949 Da / Num. of mol.: 2 / Mutation: D388N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: K12 / Gene: opgD / Production host: ![]() ![]() ![]() |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D- ...beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose Type: oligosaccharide ![]() Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D- ...beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose Type: oligosaccharide ![]() Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 569 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ![]() #5: Chemical | ChemComp-PGE / | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.04 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: MMT (pH 4.0), PEG1500, Beta-1,2-glucan |
-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: Mar 23, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.06→47.74 Å / Num. obs: 66585 / % possible obs: 99.3 % / Redundancy: 6.5 % / CC1/2: 0.996 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.06→2.11 Å / Num. unique obs: 4130 / CC1/2: 0.697 |
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Processing
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Refinement | Method to determine structure![]() ![]() Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.845 Å2
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Refinement step | Cycle: LAST / Resolution: 2.06→47.74 Å
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Refine LS restraints |
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LS refinement shell |
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