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- PDB-2zmn: Crystal Structure of basic winged bean lectin in complex with Gal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zmn | |||||||||
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Title | Crystal Structure of basic winged bean lectin in complex with Gal-alpha- 1,6 Glc | |||||||||
![]() | Basic agglutinin | |||||||||
![]() | SUGAR BINDING PROTEIN / Legume lectins / Sugar Specificity / Winged bean lectin | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Kulkarni, K.A. / Katiyar, S. / Surolia, A. / Vijayan, M. / Suguna, K. | |||||||||
![]() | ![]() Title: Structure and sugar-specificity of basic winged-bean lectin: structures of new disaccharide complexes and a comparative study with other known disaccharide complexes of the lectin. Authors: Kulkarni, K.A. / Katiyar, S. / Surolia, A. / Vijayan, M. / Suguna, K. #1: ![]() Title: Structural basis for the carbohydrate-specificity of basic winged-bean lectin and its differential affinity for Gal and GalNAc Authors: Kulkarni, K.A. / Katiyar, S. / Surolia, A. / Vijayan, M. / Suguna, K. #2: ![]() Title: Generation of blood group specificity: New insights from structural studies on the complexes of A- and B-reactive saccharides with basic winged bean agglutinin. Authors: Kulkarni, K.A. / Katiyar, S. / Surolia, A. / Vijayan, M. / Suguna, K. #3: ![]() Title: Carbohydrate specificity and quaternary association in basic winged bean lectin: X-ray analysis of the lectin at 2.5 A resolution Authors: Prabu, M.M. / Sankarnarayanan, R. / Puri, K.D. / Sharma, V. / Surolia, A. / Vijayan, M. / Suguna, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.9 KB | Display | ![]() |
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PDB format | ![]() | 162.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2zmkC ![]() 2zmlC ![]() 1wblS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 26505.604 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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-Sugars , 5 types, 11 molecules
#2: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #3: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-galactopyranose-(1-6)-beta-D-glucopyranose ![]() Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | ![]() Source method: isolated from a genetically manipulated source #6: 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 |
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-Non-polymers , 3 types, 112 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-MN / #8: Chemical | ChemComp-CA / #9: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.11 % |
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Crystal grow![]() | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 6-7% PEG 4000, 5% isopropenol, 20mM PBS, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.9→30 Å / Num. all: 23988 / Num. obs: 23768 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 43.1 Å2 / Rmerge(I) obs: 0.124 / Rsym value: 0.131 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2335 / Rsym value: 0.496 / % possible all: 98.2 |
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Processing
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Refinement | Starting model: 1WBL Resolution: 2.9→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2448478.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.2351 Å2 / ksol: 0.289404 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
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Xplor file |
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