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Open data
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Basic information
Entry | Database: PDB / ID: 1dbn | |||||||||
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Title | MAACKIA AMURENSIS LEUKOAGGLUTININ (LECTIN) WITH SIALYLLACTOSE | |||||||||
![]() | PROTEIN (LEUKOAGGLUTININ) | |||||||||
![]() | SUGAR BINDING PROTEIN / PLANT LECTIN / CARBOHYDRATE BINDING / SIALYLLACTOSE | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Imberty, A. / Gautier, C. / Lescar, J. / Loris, R. | |||||||||
![]() | ![]() Title: An unusual carbohydrate binding site revealed by the structures of two Maackia amurensis lectins complexed with sialic acid-containing oligosaccharides. Authors: Imberty, A. / Gautier, C. / Lescar, J. / Perez, S. / Wyns, L. / Loris, R. #1: ![]() Title: Sialic Acid-binding Motif of Maackia Amurensis Lectins Authors: Yamamoto, K. / Konami, Y. / Irimura, T. #2: ![]() Title: Studies on Hemagglutinins from Maackia Amurensis Seeds Authors: Kawaguchi, T. / Matsumoto, I. / Osawa, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.6 KB | Display | ![]() |
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PDB format | ![]() | 83.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25987.615 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SEEDS / Source: (natural) ![]() |
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-Sugars , 2 types, 7 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 34 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.6 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG 1000, PEG 8000, sialyllactose, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 48 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 6, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.936 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→30 Å / Num. all: 171599 / Num. obs: 171599 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 99.6 % / Biso Wilson estimate: 41.17 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 14.49 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 99.9 % / Rmerge(I) obs: 0.442 / Num. unique all: 16277 / % possible all: 99.9 |
Reflection | *PLUS Num. obs: 16436 / Num. measured all: 171599 |
Reflection shell | *PLUS % possible obs: 99.9 % / Num. unique obs: 1618 / Num. measured obs: 17687 / Mean I/σ(I) obs: 4.78 |
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Processing
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Refinement | Resolution: 2.75→30 Å / σ(F): 0 / σ(I): 0.001
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Refinement step | Cycle: LAST / Resolution: 2.75→30 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.404 / Rfactor Rwork: 0.316 |