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Open data
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Basic information
Entry | Database: PDB / ID: 3om5 | ||||||
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Title | Crystal structure of B. megaterium levansucrase mutant N252A | ||||||
![]() | Levansucrase | ||||||
![]() | TRANSFERASE / five fold beta-propeller / levansucrase | ||||||
Function / homology | ![]() levansucrase / levansucrase activity / carbohydrate utilization / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Strube, C.P. / Homann, A. / Gamer, M. / Jahn, D. / Seibel, J. / Heinz, D.W. | ||||||
![]() | ![]() Title: Polysaccharide Synthesis of the Levansucrase SacB from Bacillus megaterium Is Controlled by Distinct Surface Motifs. Authors: Strube, C.P. / Homann, A. / Gamer, M. / Jahn, D. / Seibel, J. / Heinz, D.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 | ![]() | 381.7 KB | Display | ![]() |
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PDB format | ![]() | 307.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 893.2 KB | Display | ![]() |
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Full document | ![]() | 914.8 KB | Display | |
Data in XML | ![]() | 75.2 KB | Display | |
Data in CIF | ![]() | 106.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 51029.879 Da / Num. of mol.: 4 / Fragment: Levansucrase SacB, UNP residues 29-484 / Mutation: N252A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 1171 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.1 Details: USING 3 uL OF A 8 MG/ML PROTEIN SOLUTION MIXED WITH 3 uL RESERVOIR BUFFER (0.1 M Na-Phosphate-citrate pH 4.1; 0.2 M lithiumsulfate; 20% (w/v) PEG 1000) IN THE DROPLET. , VAPOR DIFFUSION, ...Details: USING 3 uL OF A 8 MG/ML PROTEIN SOLUTION MIXED WITH 3 uL RESERVOIR BUFFER (0.1 M Na-Phosphate-citrate pH 4.1; 0.2 M lithiumsulfate; 20% (w/v) PEG 1000) IN THE DROPLET. , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||
Detector | Type: MX225 (Rayonics LLC) / Detector: CCD / Date: Aug 21, 2008 | |||||||||||||||||||||||||
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 | |||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.95→50.01 Å / Num. all: 117898 / Num. obs: 117544 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 | |||||||||||||||||||||||||
Reflection shell | Resolution: 1.95→2.11 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 51.84 Å2 / Biso mean: 25.7455 Å2 / Biso min: 10.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.955→2.006 Å / Total num. of bins used: 20
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