+Open data
-Basic information
Entry | Database: PDB / ID: 2tep | ||||||||||||
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Title | PEANUT LECTIN COMPLEXED WITH T-ANTIGENIC DISACCHARIDE | ||||||||||||
Components | PROTEIN (PEANUT LECTIN) | ||||||||||||
Keywords | LECTIN / LEGUME LECTIN / WATER BRIDGES / CARBOHYDRATE SPECIFICITY / T-ANTIGEN / PROTEIN CRYSTALLOGRAPHY / AGGLUTININ | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Arachis hypogaea (peanut) | ||||||||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.5 Å | ||||||||||||
Authors | Ravishankar, R. / Ravindran, M. / Suguna, K. / Surolia, A. / Vijayan, M. | ||||||||||||
Citation | Journal: Curr.Sci. / Year: 1997 Title: The Specificity of Peanut Agglutinin for Thomsen-Friedenreich Antigen is Mediated by Water-Bridges Authors: Ravishankar, R. / Ravindran, M. / Suguna, K. / Surolia, A. / Vijayan, M. #1: Journal: PROG.BIOPHYS.MOL.BIOL. / Year: 1996 Title: Crystal Structure of Peanut Agglutinin-T-Antigen Complex Authors: Ravishankar, R. / Ravindran, M. / Suguna, K. / Vijayan, A.S. #2: Journal: J.Mol.Biol. / Year: 1996 Title: Conformation, protein-carbohydrate interactions and a novel subunit association in the refined structure of peanut lectin-lactose complex. Authors: Banerjee, R. / Das, K. / Ravishankar, R. / Suguna, K. / Surolia, A. / Vijayan, M. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: Crystal structure of peanut lectin, a protein with an unusual quaternary structure. Authors: Banerjee, R. / Mande, S.C. / Ganesh, V. / Das, K. / Dhanaraj, V. / Mahanta, S.K. / Suguna, K. / Surolia, A. / Vijayan, M. #4: Journal: FEBS Lett. / Year: 1983 Title: Preparation and Preliminary X-Ray Studies of Three Acidic pH Crystal Forms of the Anti-T Lectin from Peanut (Arachis Hypogaea) Authors: Salunke, D.M. / Khan, M.I. / Surolia, A. / Vijayan, M. #5: Journal: J.Mol.Biol. / Year: 1982 Title: Crystallization and preliminary X-ray studies of the anti-T lectin from peanut (Arachis hypogaea). Authors: Salunke, D.M. / Khan, M.I. / Surolia, A. / Vijayan, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2tep.cif.gz | 195.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2tep.ent.gz | 156.2 KB | Display | PDB format |
PDBx/mmJSON format | 2tep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2tep_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 2tep_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 2tep_validation.xml.gz | 41.2 KB | Display | |
Data in CIF | 2tep_validation.cif.gz | 58.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/2tep ftp://data.pdbj.org/pub/pdb/validation_reports/te/2tep | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 25208.955 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: UniProt: LECG_ARAHY, UniProt: P02872*PLUS #2: Polysaccharide | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-MN / #5: 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: 3.12 Å3/Da / Density % sol: 60.58 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→99 Å / Num. obs: 33952 / % possible obs: 82 % / Redundancy: 1.94 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.128 |
Reflection | *PLUS Num. measured all: 65934 |
-Processing
Software | Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER / Resolution: 2.5→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: FREE R / σ(F): 2 Details: THERE IS A TETRAMER IN THE ASYMMETRIC UNIT WITHOUT 222 OR FOUR-FOLD SYMMETRY.
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Displacement parameters | Biso mean: 12.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.65 Å / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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