+Open data
-Basic information
Entry | Database: PDB / ID: 4ion | ||||||
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Title | Macrolepiota procera ricin B-like lectin (MPL) | ||||||
Components | Ricin B-like lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / beta-trefoil / Macrolepiota procera ricin B-like lectin (MPL) / glycans | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Macrolepiota procera (parasol mushroom) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Renko, M. / Zurga, S. / Sabotic, J. / Pohleven, J. / Kos, J. / Turk, D. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Macrolepiota procera ricin B-like lectin (MPL) Authors: Renko, M. / Zurga, S. / Sabotic, J. / Pohleven, J. / Kos, J. / Turk, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ion.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ion.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ion.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ion_validation.pdf.gz | 434.5 KB | Display | wwPDB validaton report |
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Full document | 4ion_full_validation.pdf.gz | 436.2 KB | Display | |
Data in XML | 4ion_validation.xml.gz | 18 KB | Display | |
Data in CIF | 4ion_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/4ion ftp://data.pdbj.org/pub/pdb/validation_reports/io/4ion | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15802.239 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macrolepiota procera (parasol mushroom) Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F6KMV5 #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: 2.98 Å3/Da / Density % sol: 58.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.04 M KH2phosphate, 12 %(w/v) PEG 8000, 20 %(v/v) Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Sep 10, 2012 / Details: mirrors |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→38.16 Å / Num. all: 50651 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 8 % / Rmerge(I) obs: 0.788 / Mean I/σ(I) obs: 1.91 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: partial model, obtained by iodine SAD Resolution: 1.6→38.16 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2177 / WRfactor Rwork: 0.1804 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8656 / SU B: 1.794 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0827 / SU Rfree: 0.0869 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 65.13 Å2 / Biso mean: 20.2892 Å2 / Biso min: 7.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→38.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.599→1.641 Å / Total num. of bins used: 20
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