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Yorodumi- PDB-5vbk: Crystal structure of a galactose-binding Lectin from Mytilus cali... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vbk | ||||||
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Title | Crystal structure of a galactose-binding Lectin from Mytilus californianus | ||||||
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 / Galactose-binding lectin Function and homology information | ||||||
Biological species | Mytilus californianus (California mussel) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.788 Å | ||||||
Authors | Hernandez-Santoyo, A. / Garcia-Maldonado, E. | ||||||
Citation | 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 | 5vbk.cif.gz | 78.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vbk.ent.gz | 58.1 KB | Display | PDB format |
PDBx/mmJSON format | 5vbk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vbk_validation.pdf.gz | 439.8 KB | Display | wwPDB validaton report |
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Full document | 5vbk_full_validation.pdf.gz | 441.4 KB | Display | |
Data in XML | 5vbk_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 5vbk_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/5vbk ftp://data.pdbj.org/pub/pdb/validation_reports/vb/5vbk | HTTPS FTP |
-Related structure data
Related structure data | 3wmvS S: Starting model for refinement |
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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: 16943.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mytilus californianus (California mussel) / References: UniProt: A0A0P0E482 #2: Chemical | ChemComp-GOL / #3: 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: 43.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M potassium thiocyanate, 0.1 M Bis-Tris Propane pH 8.5, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 101 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. obs: 26332 / % possible obs: 95.06 % / Redundancy: 4.4 % / CC1/2: 0.85 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.04 / Net I/σ(I): 28.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WMV Resolution: 1.788→35.088 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.788→35.088 Å
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Refine LS restraints |
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LS refinement shell |
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