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Open data
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Basic information
Entry | Database: PDB / ID: 1v6o | ||||||
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Title | Peanut lectin complexed with 10mer peptide (PVRIWSSATG) | ||||||
![]() | Galactose-binding lectin | ||||||
![]() | SUGAR BINDING PROTEIN / ![]() ![]() | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kundhavai Natchiar, S. / Arockia Jeyaprakash, A. / Ramya, T.N.C. / Thomas, C.J. / Suguna, K. / Surolia, A. / Vijayan, M. | ||||||
![]() | ![]() Title: Structural plasticity of peanut lectin: an X-ray analysis involving variation in pH, ligand binding and crystal structure. Authors: Kundhavai Natchiar, S. / Arockia Jeyaprakash, A. / Ramya, T.N. / Thomas, C.J. / Suguna, K. / Surolia, A. / Vijayan, M. #1: ![]() Title: Crystal structures of the peanut lectin-lactose complex at acidic pH: retention of unusual quaternary structure, empty and carbohydrate bound combining sites, molecular mimicry and crystal ...Title: Crystal structures of the peanut lectin-lactose complex at acidic pH: retention of unusual quaternary structure, empty and carbohydrate bound combining sites, molecular mimicry and crystal packing directed by interactions at the combining site Authors: Ravishankar, R. / Thomas, C.J. / Suguna, K. / Surolia, A. / Vijayan, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 346 KB | Display | ![]() |
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PDB format | ![]() | 284.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1v6iC ![]() 1v6jC ![]() 1v6kC ![]() 1v6lC ![]() 1v6mC ![]() 1v6nC ![]() 1cr7S 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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Unit cell |
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Components
#1: Protein | Mass: 24706.385 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-MN / #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.44 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 293 K / Method: hanging drop method / pH: 4.6 Details: 30% PEG 8000, 0.2M Ammonium sulfate and 0.1M cacodylate pH6.5, pH 4.6, hanging drop method, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: Mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3→20 Å / Num. all: 48922 / Num. obs: 43166 / % possible obs: 95.5 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.167 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.357 / Num. unique all: 1185 / % possible all: 94 |
Reflection | *PLUS Highest resolution: 3 Å / Num. measured all: 110293 |
Reflection shell | *PLUS Highest resolution: 3 Å / % possible obs: 94 % / Num. unique obs: 1185 / Num. measured obs: 2737 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1CR7 Resolution: 3→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 113603.28 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.8286 Å2 / ksol: 0.31873 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree![]() | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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