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Yorodumi- PDB-2e7q: Crystal structure of basic winged bean lectin in complex with b b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e7q | |||||||||
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Title | Crystal structure of basic winged bean lectin in complex with b blood group trisaccharide | |||||||||
Components | Basic agglutinin | |||||||||
Keywords | SUGAR BINDING PROTEIN / WINGED BEAN / JELLY ROLL | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Psophocarpus tetragonolobus (winged bean) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | |||||||||
Authors | Kulkarni, K.A. / Katiyar, S. / Surolia, A. / Vijayan, M. / Suguna, K. | |||||||||
Citation | Journal: Proteins / Year: 2007 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. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006 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: Journal: J.Mol.Biol. / Year: 1998 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. / Sankaranarayanan, R. / Puri, K.D. / Sharma, V. / Surolia, A. / Vijayan, M. / Suguna, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e7q.cif.gz | 205.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e7q.ent.gz | 164.7 KB | Display | PDB format |
PDBx/mmJSON format | 2e7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/2e7q ftp://data.pdbj.org/pub/pdb/validation_reports/e7/2e7q | HTTPS FTP |
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-Related structure data
Related structure data | 2e51C 2e53C 2e7tC 1wblS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | IT IS A HOMO-DIMER. IN THE ASYMMETRIC UNIT THERE ARE TWO MOLECULES WITH CHAINS A&B AND C&D, FORMING TWO DIMERS. |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 26014.109 Da / Num. of mol.: 4 / Fragment: UNP residues 2-238 / Source method: isolated from a natural source / Source: (natural) Psophocarpus tetragonolobus (winged bean) / References: UniProt: O24313 |
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-Sugars , 4 types, 11 molecules
#2: Polysaccharide | alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[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 | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)]2-acetamido-2-deoxy- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: 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, 242 molecules
#6: Chemical | ChemComp-CA / #7: Chemical | ChemComp-MN / #8: 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: 2.51 Å3/Da / Density % sol: 50.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.05 Details: 6-7%(w/v) PEG 6000, 10%(v/v) isopropenol, 20mM PBS, pH 7.05, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.548 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.548 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→30 Å / Num. obs: 27614 / % possible obs: 96.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 64.9 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB RNTRY 1WBL Resolution: 2.75→29.74 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2119417.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: crystals were isomorphous to 1wbl. therefore, the protein atoms from this structure were directly taken for the refinement.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.8891 Å2 / ksol: 0.293828 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→29.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.85 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
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Xplor file |
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