[English] 日本語
Yorodumi- PDB-3ef2: Structure of the Marasmius oreades mushroom lectin (MOA) in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ef2 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the Marasmius oreades mushroom lectin (MOA) in complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium. | |||||||||
Components | Agglutinin | |||||||||
Keywords | SUGAR BINDING PROTEIN / lectin / beta-trefoil / calcium-binding / carbohydrate-binding / sugar-binding | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Marasmius oreades (fairy-ring mushroom) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Grahn, E.M. / Goldstein, I.J. / Krengel, U. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structural Characterization of a Lectin from the Mushroom Marasmius oreades in Complex with the Blood Group B Trisaccharide and Calcium. Authors: Grahn, E.M. / Winter, H.C. / Tateno, H. / Goldstein, I.J. / Krengel, U. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ef2.cif.gz | 280.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ef2.ent.gz | 225.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ef2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ef2_validation.pdf.gz | 5.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ef2_full_validation.pdf.gz | 5.1 MB | Display | |
Data in XML | 3ef2_validation.xml.gz | 55.7 KB | Display | |
Data in CIF | 3ef2_validation.cif.gz | 85.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/3ef2 ftp://data.pdbj.org/pub/pdb/validation_reports/ef/3ef2 | HTTPS FTP |
-Related structure data
Related structure data | 2ihoS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 32376.707 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marasmius oreades (fairy-ring mushroom) Production host: Escherichia coli (E. coli) / References: UniProt: Q8X123 |
---|
-Sugars , 2 types, 12 molecules
#2: Polysaccharide | alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose Source method: isolated from a genetically manipulated source |
---|
-Non-polymers , 3 types, 1278 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-ACT / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.53 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Hepes, 18% PEG 8000, 0.2M calcium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 22, 2007 |
Radiation | Monochromator: Diamond, Ge / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→46 Å / Num. all: 151438 / Num. obs: 151438 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 3.3 / Num. unique all: 21953 / % possible all: 98.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IHO Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.924 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.101 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.756 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
|