+Open data
-Basic information
Entry | Database: PDB / ID: 1qf3 | ||||||
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Title | PEANUT LECTIN COMPLEXED WITH METHYL-BETA-GALACTOSE | ||||||
Components | PROTEIN (PEANUT LECTIN) | ||||||
Keywords | SUGAR BINDING PROTEIN / LECTIN / LEGUME LECTIN / WATER BRIDGES / CARBOHYDRATE SPECIFICITY / METHYL-BETA- GALACTOSE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Arachis hypogaea (peanut) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.8 Å | ||||||
Authors | Ravishankar, R. / Suguna, K. / Surolia, A. / Vijayan, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 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. #1: 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. #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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qf3.cif.gz | 189.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qf3.ent.gz | 152 KB | Display | PDB format |
PDBx/mmJSON format | 1qf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qf3_validation.pdf.gz | 465.3 KB | Display | wwPDB validaton report |
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Full document | 1qf3_full_validation.pdf.gz | 476.5 KB | Display | |
Data in XML | 1qf3_validation.xml.gz | 38.4 KB | Display | |
Data in CIF | 1qf3_validation.cif.gz | 53.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/1qf3 ftp://data.pdbj.org/pub/pdb/validation_reports/qf/1qf3 | HTTPS FTP |
-Related structure data
-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: P02872 #2: Sugar | ChemComp-MBG / #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: 3.13 Å3/Da / Density % sol: 60.69 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: HANGING DROP OF 5 MG/ML PROTEIN IN 0.05 M SODIUM PHOSPHATE BUFFER,PH 7.0, CONTAINING 0.2M SODIUM CHLORIDE, 0.02 % SODIUM AZIDE, 1.5-10MM METHYL-BETA- GALACTOSE AND 12% (W/V) PEG 8000 IN THE ...Details: HANGING DROP OF 5 MG/ML PROTEIN IN 0.05 M SODIUM PHOSPHATE BUFFER,PH 7.0, CONTAINING 0.2M SODIUM CHLORIDE, 0.02 % SODIUM AZIDE, 1.5-10MM METHYL-BETA- GALACTOSE AND 12% (W/V) PEG 8000 IN THE SAME BUFFER, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→99 Å / Num. obs: 31250 / % possible obs: 96.5 % / Redundancy: 18.3 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.128 |
Reflection | *PLUS Num. measured all: 573611 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB2PEL.ENT WITHOUT SUGAR AND WATER Resolution: 2.8→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 Details: THERE IS A TETRAMER IN THE ASYMMETRIC UNIT WITHOUT 222 OR FOUR-FOLD SYMMETRY.
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Displacement parameters | Biso mean: 19.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 4 % / Rfactor obs: 0.195 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.34 / % reflection Rfree: 3.7 % / Rfactor Rwork: 0.261 |