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Yorodumi- PDB-2qqw: Crystal structure of a cell-wall invertase (D23A) from Arabidopsi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qqw | |||||||||
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Title | Crystal structure of a cell-wall invertase (D23A) from Arabidopsis thaliana in complex with sucrose | |||||||||
Components | Beta-fructofuranosidaseSucrase | |||||||||
Keywords | HYDROLASE / invertase / Glycosidase | |||||||||
Function / homology | Function and homology information beta-fructofuranosidase activity / beta-fructofuranosidase / apoplast / defense response to fungus / response to wounding / carbohydrate metabolic process / plasma membrane Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å | |||||||||
Authors | Lammens, W. / Le Roy, K. / Van Laere, A. / Rabijns, A. / Van den Ende, W. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Crystal structures of Arabidopsis thaliana cell-wall invertase mutants in complex with sucrose. Authors: Lammens, W. / Le Roy, K. / Van Laere, A. / Rabijns, A. / Van den Ende, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qqw.cif.gz | 125.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qqw.ent.gz | 94.7 KB | Display | PDB format |
PDBx/mmJSON format | 2qqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/2qqw ftp://data.pdbj.org/pub/pdb/validation_reports/qq/2qqw | HTTPS FTP |
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-Related structure data
Related structure data | 2qquC 2qqvC 2ac1S 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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 61059.023 Da / Num. of mol.: 1 / Mutation: D23A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ATBFRUCT1 / Production host: Pichia pastoris (fungus) / References: UniProt: Q43866, beta-fructofuranosidase |
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-Sugars , 4 types, 4 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-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 |
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
#4: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose / |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 23 molecules
#6: Chemical | ChemComp-ZN / #7: 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: 2.68 Å3/Da / Density % sol: 54.02 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M sodium cacodylate, 0.1M zinc acetate, 22.5% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.0332 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 22, 2006 |
Radiation | Monochromator: Fixed exit double crystal Si [111], horizontally focussing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 15532 / Num. obs: 12825 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.41 / Redundancy: 3.4 % |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 3.3 % / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2AC1 Resolution: 2.8→28.57 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.898 / SU B: 15.384 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R Free: 0.395 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.498 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→28.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.87 Å / Total num. of bins used: 20
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