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Yorodumi- PDB-6rv5: X-ray structure of the levansucrase from Erwinia tasmaniensis in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rv5 | |||||||||
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Title | X-ray structure of the levansucrase from Erwinia tasmaniensis in complex with levanbiose | |||||||||
Components | Levansucrase (Beta-D-fructofuranosyl transferase) | |||||||||
Keywords | TRANSFERASE / Levansucrase / levanbiose / Fructosyltransferase / Fructans production. | |||||||||
Function / homology | Function and homology information levansucrase / levansucrase activity / carbohydrate utilization / metal ion binding Similarity search - Function | |||||||||
Biological species | Erwinia tasmaniensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | |||||||||
Authors | Polsinelli, I. / Caliandro, R. / Demitri, N. / Benini, S. | |||||||||
Citation | Journal: Int J Mol Sci / Year: 2019 Title: The Structure of Sucrose-Soaked Levansucrase Crystals fromErwinia tasmaniensisreveals a Binding Pocket for Levanbiose. Authors: Polsinelli, I. / Caliandro, R. / Demitri, N. / Benini, S. #1: Journal: Int.J.Biol.Macromol. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rv5.cif.gz | 207.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rv5.ent.gz | 162.6 KB | Display | PDB format |
PDBx/mmJSON format | 6rv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/6rv5 ftp://data.pdbj.org/pub/pdb/validation_reports/rv/6rv5 | HTTPS FTP |
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-Related structure data
Related structure data | 6frwS S: Starting model for refinement |
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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: 46139.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Erwinia tasmaniensis (strain DSM 17950 / CIP 109463 / Et1/99) (bacteria) Strain: DSM 17950 / CIP 109463 / Et1/99 / Gene: lsc, ETA_34670 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2VCC3, levansucrase | ||||
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#2: Polysaccharide | beta-D-fructofuranose-(2-6)-beta-D-fructofuranose / levanbiose | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | #5: 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: 2.58 Å3/Da / Density % sol: 52.36 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 28% Glycerol, 14% PEG 4000, 1.5mM Manganese(II) chloride tetrahydrate, 1.5 mM Cobalt(II) chloride hexahydrate , 1.5 mM Nickel(II) chloride hexahydrate, 1.5 mM Zinc acetate dihydrate crystals ...Details: 28% Glycerol, 14% PEG 4000, 1.5mM Manganese(II) chloride tetrahydrate, 1.5 mM Cobalt(II) chloride hexahydrate , 1.5 mM Nickel(II) chloride hexahydrate, 1.5 mM Zinc acetate dihydrate crystals soaked in Sucrose 500 mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→90.42 Å / Num. obs: 66162 / % possible obs: 99.47 % / Redundancy: 1.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.02668 / Rpim(I) all: 0.02668 / Rrim(I) all: 0.03773 / Net I/σ(I): 2.04 |
Reflection shell | Resolution: 1.58→1.64 Å / Rmerge(I) obs: 0.2867 / Num. unique obs: 6517 / CC1/2: 0.888 / Rpim(I) all: 0.2867 / Rrim(I) all: 0.4055 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FRW Resolution: 1.58→45.26 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.966 / Cross valid method: THROUGHOUT / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 23.661 Å2 | ||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.58→45.26 Å
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LS refinement shell | Resolution: 1.58→1.621 Å
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