+Open data
-Basic information
Entry | Database: PDB / ID: 2ef6 | |||||||||
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Title | Canavalia gladiata lectin complexed with Man1-3Man-OMe | |||||||||
Components | Concanavalin A | |||||||||
Keywords | PLANT PROTEIN / Canavalia gladiata / lectin / seeds / dimannosides | |||||||||
Function / homology | Function and homology information regulation of defense response to virus / monosaccharide binding / D-mannose binding / positive regulation of cell division / positive regulation of mitotic nuclear division / negative regulation of DNA-templated transcription / metal ion binding Similarity search - Function | |||||||||
Biological species | Canavalia gladiata (sword bean) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Moreno, F.B.M.B. / Bezerra, G.A. / Oliveira, T.M. / de Souza, E.P. / da Rocha, B.A.M. / Benevides, R.G. / Delatorre, P. / Cavada, B.S. / de Azevedo Jr., W.F. | |||||||||
Citation | Journal: J.Struct.Biol. / Year: 2007 Title: Structural analysis of Canavalia maritima and Canavalia gladiata lectins complexed with different dimannosides: New insights into the understanding of the structure-biological activity ...Title: Structural analysis of Canavalia maritima and Canavalia gladiata lectins complexed with different dimannosides: New insights into the understanding of the structure-biological activity relationship in legume lectins Authors: Bezerra, G.A. / Oliveira, T.M. / Moreno, F.B.M.B. / de Souza, E.P. / da Rocha, B.A.M. / Benevides, R.G. / Delatorre, P. / de Azevedo Jr., W.F. / Cavada, B.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ef6.cif.gz | 200 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ef6.ent.gz | 158.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ef6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/2ef6 ftp://data.pdbj.org/pub/pdb/validation_reports/ef/2ef6 | HTTPS FTP |
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-Related structure data
Related structure data | 2ovuC 2ow4C 2p2kC 2p34C 2p37C 1wuvS 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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-Components
#1: Protein | Mass: 25563.322 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Canavalia gladiata (sword bean) / Tissue: seed / References: UniProt: P14894 #2: Polysaccharide | alpha-D-mannopyranose-(1-3)-methyl alpha-D-mannopyranoside Source method: isolated from a genetically manipulated source #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: 2.19 Å3/Da / Density % sol: 43.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: Sodium Formate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.43 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Apr 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.43 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→40.29 Å / Num. obs: 48437 / Redundancy: 2.5 % / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 10.7 |
Reflection shell | Highest resolution: 2.07 Å / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 2 / Rsym value: 0.452 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WUV Resolution: 2.1→33.92 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.188 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.923 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→33.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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