+Open data
-Basic information
Entry | Database: PDB / ID: 3om6 | ||||||
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Title | Crystal structure of B. megaterium levansucrase mutant Y247A | ||||||
Components | Levansucrase | ||||||
Keywords | TRANSFERASE / five fold beta-propeller / levansucrase | ||||||
Function / homology | Function and homology information levansucrase / levansucrase activity / carbohydrate utilization / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus megaterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Strube, C.P. / Homann, A. / Gamer, M. / Jahn, D. / Seibel, J. / Heinz, D.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3om6.cif.gz | 380.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3om6.ent.gz | 307.4 KB | Display | PDB format |
PDBx/mmJSON format | 3om6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3om6_validation.pdf.gz | 481.4 KB | Display | wwPDB validaton report |
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Full document | 3om6_full_validation.pdf.gz | 496.9 KB | Display | |
Data in XML | 3om6_validation.xml.gz | 74 KB | Display | |
Data in CIF | 3om6_validation.cif.gz | 106.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/3om6 ftp://data.pdbj.org/pub/pdb/validation_reports/om/3om6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 50980.809 Da / Num. of mol.: 4 / Fragment: Levansucrase SacB, UNP residues 29-484 / Mutation: Y247A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: sacB / Production host: Escherichia coli (E. coli) / References: UniProt: D5DC07, levansucrase #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-PGE / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.02 % |
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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: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å | |||||||||||||||||||||||||
Detector | Type: MX-225 (Rayonics LLC) / Detector: CCD / Date: Apr 24, 2009 | |||||||||||||||||||||||||
Radiation | Monochromator: Si-111 crystal / 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: 1.96→50.01 Å / Num. all: 118542 / Num. obs: 118067 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 | |||||||||||||||||||||||||
Reflection shell | Resolution: 1.96→2.11 Å / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→50.01 Å / Cor.coef. Fo:Fc: 0.863 / Cor.coef. Fo:Fc free: 0.863 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.396 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.76 Å2 / Biso mean: 14.3256 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.009 Å / Total num. of bins used: 20
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