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Yorodumi- PDB-2dty: Crystal structure of basic winged bean lectin complexed with N-ac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dty | |||||||||
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Title | Crystal structure of basic winged bean lectin complexed with N-acetyl-D-galactosamine | |||||||||
Components | Basic agglutinin | |||||||||
Keywords | SUGAR BINDING PROTEIN / Legume lectin / GLYCOSYLATED PROTEIN / AGGLUTININ | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Psophocarpus tetragonolobus (winged bean) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.65 Å | |||||||||
Authors | Kulkarni, K.A. / Katiyar, S. / Surolia, A. / Vijayan, M. / Suguna, K. | |||||||||
Citation | 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. #1: 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. #2: Journal: Febs Lett. / Year: 2005 Title: Structural basis for the specificity of basic winged bean lectin for the Tn-antigen: a crystallographic, thermodynamic and modelling study Authors: Kulkarni, K.A. / Surolia, A. / Vijayan, M. / Suguna, K. #3: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 1999 Title: Structure of basic winged-bean lectin and a comparison with its saccharide-bound form Authors: Manoj, N. / Srinivas, V.R. / 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 | 2dty.cif.gz | 209.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dty.ent.gz | 167.7 KB | Display | PDB format |
PDBx/mmJSON format | 2dty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/2dty ftp://data.pdbj.org/pub/pdb/validation_reports/dt/2dty | HTTPS FTP |
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-Related structure data
Related structure data | 2dtwC 2du0C 2du1C 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 | Biological assembly is a dimer formed by the subunits A&B and C&D. |
-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) Psophocarpus tetragonolobus (winged bean) / References: UniProt: O24313 |
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-Sugars , 4 types, 12 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 | 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 #4: Polysaccharide | beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...beta-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 #5: Sugar | ChemComp-A2G / |
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-Non-polymers , 3 types, 284 molecules
#6: Chemical | ChemComp-MN / #7: Chemical | ChemComp-CA / #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: 51.02 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 20% PEG 4000, 10% Iso propenol, 0.02M PBS, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2000 / Details: Osmic mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→30 Å / Num. all: 30930 / Num. obs: 30930 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 51.1 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2977 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Starting model: PDB entry 1wbl Resolution: 2.65→25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2124577.19 / 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: 54.1606 Å2 / ksol: 0.347454 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.74 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
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Xplor file |
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