+Open data
-Basic information
Entry | Database: PDB / ID: 4eqv | ||||||
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Title | Structure of Saccharomyces cerevisiae invertase | ||||||
Components | Invertase 2 | ||||||
Keywords | HYDROLASE / Glycosidase GH32 / Beta-Propeller / Carbohydrate/Sugar Binding | ||||||
Function / homology | Function and homology information fructan catabolic process / inulin catabolic process / inulinase activity / raffinose catabolic process / beta-fructofuranosidase activity / beta-fructofuranosidase / sucrose alpha-glucosidase activity / sucrose catabolic process / fungal-type vacuole / cell periphery ...fructan catabolic process / inulin catabolic process / inulinase activity / raffinose catabolic process / beta-fructofuranosidase activity / beta-fructofuranosidase / sucrose alpha-glucosidase activity / sucrose catabolic process / fungal-type vacuole / cell periphery / mitochondrion / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Sainz-Polo, M.A. / Sanz-Aparicio, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Three-dimensional Structure of Saccharomyces Invertase: ROLE OF A NON-CATALYTIC DOMAIN IN OLIGOMERIZATION AND SUBSTRATE SPECIFICITY. Authors: Sainz-Polo, M.A. / Ramirez-Escudero, M. / Lafraya, A. / Gonzalez, B. / Marin-Navarro, J. / Polaina, J. / 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 | 4eqv.cif.gz | 782.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eqv.ent.gz | 651.1 KB | Display | PDB format |
PDBx/mmJSON format | 4eqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/4eqv ftp://data.pdbj.org/pub/pdb/validation_reports/eq/4eqv | HTTPS FTP |
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-Related structure data
Related structure data | 3kf3S 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 58586.242 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: SUC2, YIL162W / Plasmid: pRARE2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00724, beta-fructofuranosidase #2: Water | ChemComp-HOH / | |
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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: 4.99 Å3/Da / Density % sol: 75.35 % |
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Crystal grow | Temperature: 293 K / pH: 6.5 Details: 3% PEG 3350, 5% MPD, 0.6M Magnesium formate, 1mM TCEP, 75 mM Guanidinium chloride, 0.1 Bis-Tris pH 6.5 (2:1), VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 120 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0666 | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 29, 2011 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.0666 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 3.3→56.31 Å / Num. obs: 137870 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Biso Wilson estimate: 66.21 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 8.1 | |||||||||||||||
Reflection shell | Resolution: 3.3→3.48 Å / Redundancy: 5 % / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 2 / Rsym value: 0.377 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KF3 Resolution: 3.4→56.31 Å / Cor.coef. Fo:Fc: 0.814 / Cor.coef. Fo:Fc free: 0.787 / SU B: 23.718 / SU ML: 0.374 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 51.16 Å2
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Refinement step | Cycle: LAST / Resolution: 3.4→56.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.49 Å / Total num. of bins used: 20
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