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Yorodumi- PDB-8beu: Structure of D188A-fructofuranosidase from Rhodotorula dairenensi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8beu | ||||||
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Title | Structure of D188A-fructofuranosidase from Rhodotorula dairenensis in complex with raffinose | ||||||
Components | Beta-fructofuranosidase | ||||||
Keywords | HYDROLASE / FRUCTOFURANOSIDASE / INVERTASE / HYDROLYTIC ENZYME / GLYCOSIL HYDROLASE / PREBIOTIC / OLIGOSACCHARIDE / FRUCTOOLIGOSACCHARIDE / FOS / RHODOTORULA DAIRENENSIS | ||||||
Function / homology | Function and homology information beta-fructofuranosidase / sucrose alpha-glucosidase activity / sucrose catabolic process / fungal-type vacuole Similarity search - Function | ||||||
Biological species | Rhodotorula dairenensis (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.27 Å | ||||||
Authors | Jimenez-Ortega, E. / Sanz-Aparicio, J. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Int J Mol Sci / Year: 2022 Title: Insights into the Structure of the Highly Glycosylated Ffase from Rhodotorula dairenensis Enhance Its Biotechnological Potential. Authors: Jimenez-Ortega, E. / Narmontaite, E. / Gonzalez-Perez, B. / Plou, F.J. / Fernandez-Lobato, M. / Sanz-Aparicio, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8beu.cif.gz | 447.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8beu.ent.gz | 364 KB | Display | PDB format |
PDBx/mmJSON format | 8beu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8beu_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 8beu_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 8beu_validation.xml.gz | 81 KB | Display | |
Data in CIF | 8beu_validation.cif.gz | 111.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/8beu ftp://data.pdbj.org/pub/pdb/validation_reports/be/8beu | HTTPS FTP |
-Related structure data
Related structure data | 8beqSC 8besC 8betC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 70671.266 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodotorula dairenensis (fungus) / Gene: INV / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115 / References: UniProt: A0A856TAI5, beta-fructofuranosidase |
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-Sugars , 7 types, 50 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose #5: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-MAN / #8: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 557 molecules
#9: Chemical | ChemComp-PEG / |
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#10: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.23 Å3/Da / Density % sol: 44.92 % / Description: Bladed crystal |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% PEG 3350, 0.2 M NaCl, 0.1 M BIS-TRIS pH 5.5 at 5.5 mg ml-1 concentration, 2:1 rate. Soaking: Mother liquor solution supplemented with 30 mM raffinose. 2h Cryocooling: Mother liquor ...Details: 20% PEG 3350, 0.2 M NaCl, 0.1 M BIS-TRIS pH 5.5 at 5.5 mg ml-1 concentration, 2:1 rate. Soaking: Mother liquor solution supplemented with 30 mM raffinose. 2h Cryocooling: Mother liquor solution supplemented with 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979264 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2021 / Details: KB Mirrors |
Radiation | Monochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979264 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→46.29 Å / Num. obs: 113410 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.055 / Rrim(I) all: 0.144 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.27→2.31 Å / Redundancy: 7 % / Rmerge(I) obs: 0.689 / Num. unique obs: 5618 / CC1/2: 0.866 / Rpim(I) all: 0.401 / Rrim(I) all: 0.744 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 8BEQ Resolution: 2.27→46.29 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.396 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.328 / ESU R Free: 0.231 / 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: 135.09 Å2 / Biso mean: 47.699 Å2 / Biso min: 21.94 Å2
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Refinement step | Cycle: final / Resolution: 2.27→46.29 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.27→2.329 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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