+Open data
-Basic information
Entry | Database: PDB / ID: 8beq | ||||||
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Title | Structure of fructofuranosidase from Rhodotorula dairenensis | ||||||
Components | Fructofuranosidase from Rhodotorula dairenensis | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.07 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 | 8beq.cif.gz | 242.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8beq.ent.gz | 191 KB | Display | PDB format |
PDBx/mmJSON format | 8beq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8beq_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8beq_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8beq_validation.xml.gz | 45 KB | Display | |
Data in CIF | 8beq_validation.cif.gz | 66 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/8beq ftp://data.pdbj.org/pub/pdb/validation_reports/be/8beq | HTTPS FTP |
-Related structure data
Related structure data | 8besC 8betC 8beuC 4eqvS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: _ / Auth seq-ID: 142 - 672 / Label seq-ID: 142 - 672
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 70715.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodotorula dairenensis (fungus) / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115 / References: UniProt: A0A856TAI5 |
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-Sugars , 4 types, 27 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-MAN / #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 604 molecules
#6: Chemical | ChemComp-PEG / | ||||
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#7: Chemical | ChemComp-GOL / #8: Chemical | ChemComp-BTB / | #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 1.96 Å3/Da / Density % sol: 39.61 % / Description: Bar |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG 3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris pH 5.5. Cryocooling: mother liquor solution supplemented with 15% glycerol. 8 mg mL-1 protein concentration and 2:1 (protein: reservoir) rate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2020 / 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: 0.979257 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→47.45 Å / Num. obs: 66921 / % possible obs: 99.5 % / Redundancy: 5.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.069 / Rrim(I) all: 0.161 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.07→2.12 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 4459 / CC1/2: 0.741 / Rpim(I) all: 0.321 / Rrim(I) all: 0.742 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EQV Resolution: 2.07→47.45 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.372 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.168 / 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: 80.34 Å2 / Biso mean: 23.196 Å2 / Biso min: 10.89 Å2
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Refinement step | Cycle: final / Resolution: 2.07→47.45 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 17341 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.07→2.124 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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