[English] 日本語
![](img/lk-miru.gif)
- PDB-8hui: Crystal structure of DFA I-forming Inulin Lyase from Streptomyces... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8hui | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of DFA I-forming Inulin Lyase from Streptomyces peucetius subsp. caesius ATCC 27952 in complex with GF4, DFA I, and fructose | ||||||
![]() | Fructotransferase | ||||||
![]() | LYASE / right-handed beta-helix protein / DFA I-forming inulin lyase / complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cheng, M. / Rao, Y.J. / Mu, W.M. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Crystal structure of DFA I-forming Inulin Lyase from Streptomyces peucetius subsp. caesius ATCC 27952 in complex with GF4, DFA I, and fructose Authors: Cheng, M. / Rao, Y.J. / Mu, W.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 452.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 374.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3.1 MB | Display | |
Data in XML | ![]() | 51 KB | Display | |
Data in CIF | ![]() | 77.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 42752.516 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CGZ69_03210 / Production host: ![]() ![]() References: UniProt: A0A2D3U3Z1, inulin fructotransferase (DFA-I-forming) |
---|
-Sugars , 3 types, 7 molecules ![](data/chem/img/FRU.gif)
#2: Polysaccharide | Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Polysaccharide | beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-beta-D- ...beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 4 / Source method: isolated from a natural source #4: Sugar | ChemComp-FRU / | |
---|
-Non-polymers , 4 types, 946 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-EDO / |
---|---|
#6: Chemical | ChemComp-MES / |
#7: Chemical | ChemComp-PEG / |
#8: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.62 % |
---|---|
Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES monohydrate, 12% Polyethylene glycol 20,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→45.84 Å / Num. obs: 247198 / % possible obs: 99.7 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.105 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.44→1.49 Å / Rmerge(I) obs: 0.921 / Num. unique obs: 24175 / CC1/2: 0.837 / Rrim(I) all: 0.962 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.44→45.84 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|