+Open data
-Basic information
Entry | Database: PDB / ID: 6bfm | ||||||
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Title | Galactose-binding Lectin from Mytilus californianus, Isoform1 | ||||||
Components | Lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / GALACTOSE-BINDING LECTIN | ||||||
Function / homology | galactose binding / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta / ACETATE ION / DI(HYDROXYETHYL)ETHER / Galactose-binding lectin Function and homology information | ||||||
Biological species | Mytilus californianus (California mussel) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.488 Å | ||||||
Authors | Hernandez-Santoyo, A. / Garcia-Maldonado, E. | ||||||
Citation | Journal: To Be Published Title: Glycan-induced oligomerization of a lectin from Mytilus californianus Authors: Garcia-Maldonado, E. / Medina-Romero, Y. / Macias-Rubalcava, M.L. / Hernandez-Santoyo, A. #1: Journal: Fish Shellfish Immunol. / Year: 2017 Title: Molecular and functional characterization of a glycosylated Galactose-Binding lectin from Mytilus californianus. Authors: Garcia-Maldonado, E. / Cano-Sanchez, P. / Hernandez-Santoyo, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bfm.cif.gz | 85.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bfm.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 6bfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/6bfm ftp://data.pdbj.org/pub/pdb/validation_reports/bf/6bfm | HTTPS FTP |
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-Related structure data
Related structure data | 3wmuS S: Starting model for refinement |
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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: 17167.668 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mytilus californianus (California mussel) Tissue: Mantle / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0P0E482 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-PEG / | #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: 2.18 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 18% polyethylene glycol 4000, 50 mM sodium acetate, 0.1M HEPES, pH 7.5, 0.1M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 101 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5416 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5416 Å / Relative weight: 1 |
Reflection | Resolution: 1.488→36.56 Å / Num. obs: 48409 / % possible obs: 99.6 % / Redundancy: 9.9 % / Biso Wilson estimate: 15.03 Å2 / CC1/2: 0.819 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.027 / Net I/av σ(I): 2.8 / Net I/σ(I): 52.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WMU Resolution: 1.488→36.56 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.25
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.488→36.56 Å
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Refine LS restraints |
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LS refinement shell |
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