+Open data
-Basic information
Entry | Database: PDB / ID: 1v6o | ||||||
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Title | Peanut lectin complexed with 10mer peptide (PVRIWSSATG) | ||||||
Components | Galactose-binding lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / Lectin / agglutinin / open quaternary association / monoclinic and peptide | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Arachis hypogaea (peanut) | ||||||
Method | X-RAY DIFFRACTION / Isomorphous replacement / Resolution: 3 Å | ||||||
Authors | Kundhavai Natchiar, S. / Arockia Jeyaprakash, A. / Ramya, T.N.C. / Thomas, C.J. / Suguna, K. / Surolia, A. / Vijayan, M. | ||||||
Citation | 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: Kundhavai Natchiar, S. / Arockia Jeyaprakash, A. / Ramya, T.N. / Thomas, C.J. / Suguna, K. / Surolia, A. / Vijayan, M. #1: Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v6o.cif.gz | 346 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v6o.ent.gz | 284.5 KB | Display | PDB format |
PDBx/mmJSON format | 1v6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/1v6o ftp://data.pdbj.org/pub/pdb/validation_reports/v6/1v6o | 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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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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) Arachis hypogaea (peanut) / Tissue: seed / References: UniProt: P02872 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-MN / #4: 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: 60.44 % | ||||||||||||||||||||||||||||||||||||||||||
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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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
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: 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 |
-Processing
Software |
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Refinement | Method to determine structure: Isomorphous replacement 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: 0.241 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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