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Yorodumi- PDB-2ar6: Pterocarpus angolensis Lectin (PAL) In Complex With The Pentasacc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ar6 | |||||||||
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Title | Pterocarpus angolensis Lectin (PAL) In Complex With The Pentasaccharide M592 | |||||||||
Components | lectin | |||||||||
Keywords | SUGAR BINDING PROTEIN / LECTIN / CARBOHYDRATE RECOGNITION | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pterocarpus angolensis (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Buts, L. / Garcia-Pino, A. / Imberty, A. / Amiot, N. / Boons, G.J. / Beeckmans, S. / Versees, W. / Wyns, L. / Loris, R. | |||||||||
Citation | Journal: Febs J. / Year: 2006 Title: Structural basis for the recognition of complex-type biantennary oligosaccharides by Pterocarpus angolensis lectin. Authors: Buts, L. / Garcia-Pino, A. / Imberty, A. / Amiot, N. / Boons, G.J. / Beeckmans, S. / Versees, W. / Wyns, L. / Loris, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ar6.cif.gz | 118.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ar6.ent.gz | 89.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ar6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/2ar6 ftp://data.pdbj.org/pub/pdb/validation_reports/ar/2ar6 | HTTPS FTP |
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-Related structure data
Related structure data | 2arbC 2areC 2arxC 2auyC 1q8oS 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, 2 molecules AB
#1: Protein | Mass: 27575.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pterocarpus angolensis (plant) / Tissue: seed / References: UniProt: Q8GSD2 |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 307 molecules
#4: Chemical | #5: Chemical | #6: 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: 2.63 Å3/Da / Density % sol: 52.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG8000, 200 mM calcium acetate, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.812 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.812 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. all: 55077 / Num. obs: 54417 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.052 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.607 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1Q8O Resolution: 1.8→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Refine LS restraints |
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