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Open data
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Basic information
Entry | Database: PDB / ID: 1sbd | |||||||||
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Title | SOYBEAN AGGLUTININ COMPLEXED WITH 2,4-PENTASACCHARIDE | |||||||||
![]() | SOYBEAN AGGLUTININ | |||||||||
![]() | LECTIN / AGGLUTININ | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Dessen, A. / Olsen, L.R. / Gupta, D. / Sabesan, S. / Brewer, C.F. / Sacchettini, J.C. | |||||||||
![]() | ![]() Title: X-ray crystallographic studies of unique cross-linked lattices between four isomeric biantennary oligosaccharides and soybean agglutinin. Authors: Olsen, L.R. / Dessen, A. / Gupta, D. / Sabesan, S. / Sacchettini, J.C. / Brewer, C.F. #1: ![]() Title: X-Ray Crystal Structure of the Soybean Agglutinin Cross-Linked with a Biantennary Analog of the Blood Group I Carbohydrate Antigen Authors: Dessen, A. / Gupta, D. / Sabesan, S. / Brewer, C.F. / Sacchettini, J.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.6 KB | Display | ![]() |
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PDB format | ![]() | 41.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 783.5 KB | Display | ![]() |
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Full document | ![]() | 796.2 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27595.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-MN / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Compound details | RATHER THAN PROTEIN-PROTEIN CONTACTS, THE DOMINANT FORCE IN THESE CRYSTALS IS SACCHARIDE-PROTEIN ...RATHER THAN PROTEIN-PROTEIN CONTACTS, THE DOMINANT FORCE IN THESE CRYSTALS IS SACCHARIDE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.4 Å3/Da / Density % sol: 77 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.2 / Details: 0.1M HEPES, PH7.2,1MM CACL2,1MM MNCL2,0.15M NACL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 70 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Dessen, A., (1995) Biochemistry, 34, 4933. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Oct 9, 1994 / Details: COLLIMATOR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→99 Å / Num. obs: 18788 / % possible obs: 82 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.52→2.67 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.411 / % possible all: 54 |
Reflection | *PLUS Num. measured all: 112590 |
Reflection shell | *PLUS % possible obs: 49 % |
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Processing
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Refinement | Method to determine structure: RIGID BODY REFINEMENT VS 1SBA Resolution: 2.52→15 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: TNT / Bsol: 172 Å2 / ksol: 0.44 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.52→15 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.205 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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