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Yorodumi- PDB-3u14: Structure of D50A-fructofuranosidase from Schwanniomyces occident... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u14 | |||||||||
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Title | Structure of D50A-fructofuranosidase from Schwanniomyces occidentalis complexed with inulin | |||||||||
Components | Fructofuranosidase | |||||||||
Keywords | HYDROLASE / Glycosidase GH32 / Beta-Propeller / Carbohydrate/Sugar Binding / Glycosylations | |||||||||
Function / homology | Function and homology information beta-fructofuranosidase / sucrose alpha-glucosidase activity / sucrose catabolic process / fungal-type vacuole / metal ion binding Similarity search - Function | |||||||||
Biological species | Schwanniomyces occidentalis (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Molecular Replacement, FOURIER SYNTHESIS / Resolution: 2.24 Å | |||||||||
Authors | Sainz-Polo, M.A. / Sanz-Aparicio, J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural and kinetic insights reveal that the amino acid pair GLN228/ASN254 modulates the transfructosylating specificity of Schwanniomyces occidentalis beta-fructofuranosidase, an enzyme ...Title: Structural and kinetic insights reveal that the amino acid pair GLN228/ASN254 modulates the transfructosylating specificity of Schwanniomyces occidentalis beta-fructofuranosidase, an enzyme that produces prebiotics. Authors: Sainz-Polo, M.A. / Gonzalez-Perez, D. / Gonzalez, 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 | 3u14.cif.gz | 233.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u14.ent.gz | 186.2 KB | Display | PDB format |
PDBx/mmJSON format | 3u14.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u14_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3u14_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3u14_validation.xml.gz | 46.3 KB | Display | |
Data in CIF | 3u14_validation.cif.gz | 66.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/3u14 ftp://data.pdbj.org/pub/pdb/validation_reports/u1/3u14 | HTTPS FTP |
-Related structure data
Related structure data | 3u75C 3kf3S S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 2 / Auth seq-ID: 27 - 535 / Label seq-ID: 27 - 535
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-Components
#1: Protein | Mass: 61088.891 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schwanniomyces occidentalis (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: E5D0X5*PLUS, beta-fructofuranosidase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | Nonpolymer details | INULIN IS COMPOSED OF FRU 1000-1005 | Sequence details | THE SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN, UNIPROT P24133 HAS BEEN SUPERSEEDED BY CQ890277 ...THE SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN, UNIPROT P24133 HAS BEEN SUPERSEEDE | |
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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: 2.85 Å3/Da / Density % sol: 56.77 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 8 Details: 15% PEG 6000, 3% MPD, 0.2M MgCl2, 0.1M HCl-Tris pH 8, LIQUID DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 9, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.24→107.67 Å / Num. all: 65603 / Num. obs: 65603 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.14 / Rsym value: 0.14 |
Reflection shell | Resolution: 2.24→2.36 Å / Redundancy: 5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.3 / Num. unique all: 9367 / Rsym value: 0.5 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: Molecular Replacement, FOURIER SYNTHESIS Starting model: 3KF3 Resolution: 2.24→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.899 / SU B: 5.821 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 16.965 Å2
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Refinement step | Cycle: LAST / Resolution: 2.24→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.24→2.298 Å / Total num. of bins used: 20
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