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Open data
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Basic information
Entry | Database: PDB / ID: 1pt2 | |||||||||
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Title | Crystal structure of levansucrase (E342A) complexed with sucrose | |||||||||
![]() | Levansucrase | |||||||||
![]() | TRANSFERASE / GLYCOSIDE HYDROLASE / LEVANSUCRASE / BETA-PROPELLER / LEVAN / SUCROSE | |||||||||
Function / homology | ![]() levansucrase / levansucrase activity / carbohydrate utilization / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Meng, G. / Futterer, K. | |||||||||
![]() | ![]() Title: Structural framework of fructosyl transfer in Bacillus subtilis levansucrase Authors: Meng, G. / Futterer, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.8 KB | Display | ![]() |
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PDB format | ![]() | 76.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1oygSC 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
#1: Protein | Mass: 50264.590 Da / Num. of mol.: 1 / Mutation: E342A 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 / sucrose |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.83 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.3 / Method: microdialysis | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAC Science DIP-2030B / Detector: IMAGE PLATE / Date: Apr 1, 2003 |
Radiation | Monochromator: OSMIC CONFOCAL OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→30 Å / Num. all: 26171 / Num. obs: 26171 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.07→2.14 Å / % possible all: 96.9 |
Reflection | *PLUS Redundancy: 4 % / Num. measured all: 202902 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 96.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 29 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1oyg Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.817 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.211 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.213 Å / Total num. of bins used: 10 /
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.21 Å |