+Open data
-Basic information
Entry | Database: PDB / ID: 1pt2 | |||||||||
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Title | Crystal structure of levansucrase (E342A) complexed with sucrose | |||||||||
Components | Levansucrase | |||||||||
Keywords | TRANSFERASE / GLYCOSIDE HYDROLASE / LEVANSUCRASE / BETA-PROPELLER / LEVAN / SUCROSE | |||||||||
Function / homology | Function and homology information levansucrase / levansucrase activity / carbohydrate utilization / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Meng, G. / Futterer, K. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pt2.cif.gz | 103.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pt2.ent.gz | 76.4 KB | Display | PDB format |
PDBx/mmJSON format | 1pt2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pt2_validation.pdf.gz | 848.6 KB | Display | wwPDB validaton report |
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Full document | 1pt2_full_validation.pdf.gz | 849.2 KB | Display | |
Data in XML | 1pt2_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 1pt2_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/1pt2 ftp://data.pdbj.org/pub/pdb/validation_reports/pt/1pt2 | HTTPS FTP |
-Related structure data
Related structure data | 1oygSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Bacillus subtilis (bacteria) / Gene: SACB / Plasmid: pET11c-sacbe342a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05655, levansucrase |
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |