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- PDB-7oso: The crystal structure of Erwinia tasmaniensis levansucrase in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7oso | ||||||
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Title | The crystal structure of Erwinia tasmaniensis levansucrase in complex with (S)-1,2,4-butanentriol | ||||||
![]() | Levansucrase (Beta-D-fructofuranosyl transferase) | ||||||
![]() | TRANSFERASE / fructosyltransferase / levan / FOS / transfructosylation / fructo-oligosaccharides / oligofructans | ||||||
Function / homology | levansucrase / levansucrase activity / Glycoside hydrolase, family 68 / Levansucrase/Invertase / carbohydrate utilization / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / metal ion binding / (2~{S})-butane-1,2,4-triol / levansucrase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Polsinelli, I. / Salomone-Stagni, M. / Benini, S. | ||||||
![]() | ![]() Title: Erwinia tasmaniensis levansucrase shows enantiomer selection for (S)-1,2,4-butanetriol. Authors: Polsinelli, I. / Salomone-Stagni, M. / Benini, S. #1: ![]() Title: The Structure of Sucrose-Soaked Levansucrase Crystals from Erwinia tasmaniensis reveals a Binding Pocket for Levanbiose. Authors: Polsinelli, I. / Caliandro, R. / Demitri, N. / Benini, S. #2: ![]() Title: Comparison of the Levansucrase from the epiphyte Erwinia tasmaniensis vs its homologue from the phytopathogen Erwinia amylovora. Authors: Polsinelli, I. / Caliandro, R. / Salomone-Stagni, M. / Demitri, N. / Rejzek, M. / Field, R.A. / Benini, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.8 KB | Display | ![]() |
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PDB format | ![]() | 158.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 747.1 KB | Display | ![]() |
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Full document | ![]() | 747.3 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 33.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d47S S: Starting model for refinement |
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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
#1: Protein | Mass: 46139.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 17950 / CIP 109463 / Et1/99 / Gene: lsc, ETA_34670 Production host: ![]() ![]() References: UniProt: B2VCC3, levansucrase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-0V1 / ( | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG 3000 15%, 1,2,4-Butanetriol (CAS 3068-00-6) 20%, NDSB 256 1%, 2.5 mM Manganese(II) chloride tetrahydrate, 2.5 mM Cobalt(II) chloride hexahydrate, 2.5 mM Nickel(II) chloride hexahydrate, ...Details: PEG 3000 15%, 1,2,4-Butanetriol (CAS 3068-00-6) 20%, NDSB 256 1%, 2.5 mM Manganese(II) chloride tetrahydrate, 2.5 mM Cobalt(II) chloride hexahydrate, 2.5 mM Nickel(II) chloride hexahydrate, 2.5 mM Zinc acetate dihydrate) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→45.19 Å / Num. obs: 189742 / % possible obs: 99.91 % / Redundancy: 5.6 % / Biso Wilson estimate: 20.95 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.25 |
Reflection shell | Resolution: 1.4→1.45 Å / Num. unique obs: 30398 / CC1/2: 0.686 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4D47 Resolution: 1.4→45.19 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.117 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0474 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.047 / 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: 109.49 Å2 / Biso mean: 24.355 Å2 / Biso min: 15.31 Å2
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Refinement step | Cycle: final / Resolution: 1.4→45.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Rfactor Rfree error: 0
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