+Open data
-Basic information
Entry | Database: PDB / ID: 2pel | ||||||||||||
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Title | PEANUT LECTIN | ||||||||||||
Components | PEANUT LECTIN | ||||||||||||
Keywords | LECTIN (AGGLUTININ) / LEGUME LECTIN / OPEN QUATERNARY STRUCTURE / CARBOHYDRATE SPECIFICITY / PROTEIN CRYSTALLOGRAPHY / AGGLUTININ | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Arachis hypogaea (peanut) | ||||||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.25 Å | ||||||||||||
Authors | Banerjee, R. / Das, K. / Ravishankar, R. / Suguna, K. / Surolia, A. / Vijayan, M. | ||||||||||||
Citation | 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. #1: 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. #2: 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. #3: 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 | 2pel.cif.gz | 198 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pel.ent.gz | 157.8 KB | Display | PDB format |
PDBx/mmJSON format | 2pel.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/2pel ftp://data.pdbj.org/pub/pdb/validation_reports/pe/2pel | HTTPS FTP |
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-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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 25208.955 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: UniProt: P02872 |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | #3: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose | |
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-Non-polymers , 3 types, 571 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-MN / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: 1990 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.25 Å / Num. obs: 50764 / % possible obs: 88 % / Rmerge(I) obs: 0.079 |
Reflection | *PLUS Lowest resolution: 9999 Å / Num. measured all: 173209 |
Reflection shell | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 2.34 Å / % possible obs: 42.3 % / Num. unique obs: 4508 / Num. measured obs: 7107 / Rmerge(I) obs: 0.15 |
-Processing
Software |
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Refinement | Resolution: 2.25→10 Å / σ(F): 3 Details: THERE IS A TETRAMER IN THE ASYMMETRIC UNIT WITHOUT 222 OR FOUR-FOLD SYMMETRY.
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Displacement parameters | Biso mean: 22.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.12 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.164 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.5 Å2 |