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Yorodumi- PDB-2aey: Crystal structure of fructan 1-exohydrolase IIa from Cichorium in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aey | |||||||||
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Title | Crystal structure of fructan 1-exohydrolase IIa from Cichorium intybus in complex with 2,5 dideoxy-2,5-immino-D-mannitol | |||||||||
Components | fructan 1-exohydrolase IIa | |||||||||
Keywords | HYDROLASE / five fold beta propeller | |||||||||
Function / homology | Function and homology information fructan beta-fructosidase / fructan beta-fructosidase activity / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Cichorium intybus (chicory) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å | |||||||||
Authors | Verhaest, M. / Le Roy, K. / De Ranter, C.J. / Van Laere, A. / Van den Ende, W. / Rabijns, A. | |||||||||
Citation | Journal: New Phytol / Year: 2007 Title: Insights into the fine architecture of the active site of chicory fructan 1-exohydrolase: 1-kestose as substrate vs sucrose as inhibitor. Authors: Verhaest, M. / Lammens, W. / Le Roy, K. / De Ranter, C.J. / 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 | 2aey.cif.gz | 120.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aey.ent.gz | 91.5 KB | Display | PDB format |
PDBx/mmJSON format | 2aey.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/2aey ftp://data.pdbj.org/pub/pdb/validation_reports/ae/2aey | HTTPS FTP |
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-Related structure data
Related structure data | 2addC 2adeC 2aezC 1st8S C: citing same article (ref.) 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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-Components
#1: Protein | Mass: 61115.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cichorium intybus (chicory) / Gene: 1-feh IIa / Production host: Pichia pastoris (fungus) / References: UniProt: Q93X60, EC: 3.2.1.153 |
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#2: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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 |
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Sugar | ChemComp-DQQ / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 7.2 Å3/Da / Density % sol: 82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: sodium potassium phosphate, potassium phosphate, pH 7.0, 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 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 7, 2005 / Details: bent mirror |
Radiation | Monochromator: triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→30 Å / Num. all: 27928 / Num. obs: 21485 / % possible obs: 76.2 % / Observed criterion σ(F): 1.41 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.187 |
Reflection shell | Resolution: 3.25→3.31 Å / Rmerge(I) obs: 0.426 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ST8 Resolution: 3.27→29.7 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 106827.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.274 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.27→29.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.25→3.45 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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