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Open data
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Basic information
Entry | Database: PDB / ID: 7fdz | ||||||
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Title | Levansucrase from Brenneria sp. EniD 312 with sucrose | ||||||
![]() | Levansucrase | ||||||
![]() | TRANSFERASE / Levansucrase / fructosyltransferase / levan synthesis | ||||||
Function / homology | ![]() levansucrase / levansucrase activity / carbohydrate utilization / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, W. / Hou, X.D. / Rao, Y.J. / Pijning, T. / Guskov, A. / Mu, W.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of Levansucrase from the Gram-Negative Bacterium Brenneria Provides Insights into Its Product Size Specificity. Authors: Xu, W. / Ni, D. / Hou, X. / Pijning, T. / Guskov, A. / Rao, Y. / Mu, 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 | ![]() | 211.6 KB | Display | ![]() |
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PDB format | ![]() | 165.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 36.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ehrC ![]() 7ehsC ![]() 7ehtC ![]() 4d47S S: Starting model for refinement 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 49396.871 Da / Num. of mol.: 1 / Mutation: D68N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose |
-Non-polymers , 6 types, 562 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PE8.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PE8.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / | ||||||||
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#4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-PE8 / | #7: Chemical | ChemComp-GOL / #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→84.98 Å / Num. obs: 161790 / % possible obs: 80.7 % / Redundancy: 38.1 % / CC1/2: 1 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.18→1.2 Å / Num. unique obs: 578 / CC1/2: 0.644 / % possible all: 5.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4D47 Resolution: 1.35→84.98 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.306 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.82 Å2 / Biso mean: 15.974 Å2 / Biso min: 4.85 Å2
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Refinement step | Cycle: final / Resolution: 1.35→84.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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