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Open data
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Basic information
Entry | Database: PDB / ID: 1cq9 | ||||||
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Title | PEANUT LECTIN-TRICLINIC FORM | ||||||
![]() | PROTEIN (PEANUT LECTIN) | ||||||
![]() | LECTIN / LEGUME LECTIN / OPEN QUATERNARY STRUCTURE / TRICLINIC FORM / ACIDIC PH | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ravishankar, R. / Suguna, K. / Surolia, A. / Vijayan, M. | ||||||
![]() | ![]() 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. #1: ![]() Title: Structures of the Complexes of Peanut Lectin with Methyl-Beta-Galactose and N- Acetyllactosamine and a Comparative Study of Carbohydrate Binding in Gal/ Galnac-Specific Legume Lectins Authors: Ravishankar, R. / Suguna, K. / Surolia, A. / Vijayan, M. #2: ![]() 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. #3: ![]() 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. #4: ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.1 KB | Display | ![]() |
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PDB format | ![]() | 142.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.7 KB | Display | ![]() |
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Full document | ![]() | 451.8 KB | Display | |
Data in XML | ![]() | 33.2 KB | Display | |
Data in CIF | ![]() | 45.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1cr7C ![]() 2pelS 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: 25208.955 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-MN / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.72 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: pH 4.6 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.4 / Method: microdialysis / Details: Salunke, D.M., (1983) FEBS Lett., 156, 127. | ||||||||||||||||||||||||||||||||||||||||||
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 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→28.7 Å / Num. obs: 18342 / % possible obs: 82.32 % / Redundancy: 1.39 % / Rmerge(I) obs: 0.1572 / Net I/σ(I): 2.53 |
Reflection | *PLUS Highest resolution: 3.5 Å / Num. obs: 11935 / % possible obs: 84.3 % / Num. measured all: 16538 / Rmerge(I) obs: 0.157 |
Reflection shell | *PLUS % possible obs: 81.4 % / Rmerge(I) obs: 0.301 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2PEL WITHOUT SUGAR AND WATER Resolution: 3.5→10 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 Details: THERE IS A TETRAMER IN THE UNIT CELL WITHOUT 222 OR FOUR-FOLD SYMMETRY.
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Displacement parameters | Biso mean: 20.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.5→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAIN | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.5→3.71 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.5 Å / Lowest resolution: 10 Å / Rfactor obs: 0.217 / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.217 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.276 / Rfactor Rwork: 0.237 |