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Yorodumi- PDB-2dvf: Crystals of peanut lectin grown in the presence of GAL-ALPHA-1,3-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dvf | ||||||
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Title | Crystals of peanut lectin grown in the presence of GAL-ALPHA-1,3-GAL-BETA-1,4-GAL | ||||||
Components | Galactose-binding lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / LEGUME LECTIN / AGGLUTININ / OPEN QUATERNARY STRUCTURE / CARBOHYDRATE SPECIFICITY | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Arachis hypogaea (peanut) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.74 Å | ||||||
Authors | Natchiar, S.K. / Srinivas, O. / Mitra, N. / Surolia, A. / Jayaraman, N. / Vijayan, M. | ||||||
Citation | Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006 Title: Structural studies on peanut lectin complexed with disaccharides involving different linkages: further insights into the structure and interactions of the lectin Authors: Natchiar, S.K. / Srinivas, O. / Mitra, N. / Surolia, A. / Jayaraman, N. / 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: 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: 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. #4: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004 Title: Structural plasticity of peanut lectin: an X-ray analysis involving variation in pH, ligand binding and crystal structure Authors: Natchiar, S.K. / Jeyaprakash, A.A. / Ramya, T.N. / Thomas, C.J. / Suguna, K. / Surolia, A. / Vijayan, M. #5: Journal: Curr.Sci. / Year: 2006 Title: Multivalency in Lectins. A Crystallographic Modellin and Light-Scattering Study Involving Peanut Lectin and a Bivalent Ligand Authors: Natchiar, S.K. / Srinivas, O. / Nivedita, M. / Sagarika, D. / Jayaraman, N. / 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 | 2dvf.cif.gz | 194.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dvf.ent.gz | 155.2 KB | Display | PDB format |
PDBx/mmJSON format | 2dvf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/2dvf ftp://data.pdbj.org/pub/pdb/validation_reports/dv/2dvf | HTTPS FTP |
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-Related structure data
Related structure data | 2dv9C 2dvaC 2dvbC 2dvdC 2dvgC 2pelS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Biological Molecules is a tetramer. Asymmetric unit contains a biological unit. |
-Components
#1: Protein | Mass: 25208.955 Da / Num. of mol.: 4 / Fragment: residues 1-236 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: UniProt: P02872 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-SO4 / #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: 2.7 Å3/Da / Density % sol: 54.3 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 7.5% PEG 8000, 0.025M Sodium cadodylate, 0.5M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Monochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.74→20 Å / Num. obs: 31035 / % possible obs: 98.1 % / Redundancy: 4.7 % / Biso Wilson estimate: 59.9 Å2 / Rmerge(I) obs: 0.142 / Rsym value: 0.158 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.74→2.84 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1530 / Rsym value: 0.545 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PEL Resolution: 2.74→19.94 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1704934.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: MLF TARGET
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.4088 Å2 / ksol: 0.312253 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.74→19.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.74→2.91 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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