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Yorodumi- PDB-4iyb: Macrolepiota procera ricin B-like lectin (MPL) in complex with ga... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iyb | ||||||
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Title | Macrolepiota procera ricin B-like lectin (MPL) in complex with galactose | ||||||
Components | Ricin B-like lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / beta-trefoil / galactose / glycans | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Macrolepiota procera (parasol mushroom) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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) in complex with galactose 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 | 4iyb.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iyb.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 4iyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/4iyb ftp://data.pdbj.org/pub/pdb/validation_reports/iy/4iyb | HTTPS FTP |
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-Related structure data
Related structure data | 4ionS 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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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: Sugar | ChemComp-GAL / | #3: Chemical | ChemComp-GOL / #4: 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: 2.88 Å3/Da / Density % sol: 57.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.04 M KH2phosphate, 10 %(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: MAR CCD 165 mm / Detector: CCD / Date: Sep 10, 2012 / Details: mirrors |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→50 Å / Num. all: 50090 / Num. obs: 49337 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.59→1.62 Å / Redundancy: 9 % / Rmerge(I) obs: 0.416 / Num. unique all: 2275 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ION Resolution: 1.59→44.97 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.972 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.054 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.064 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.36 Å2 / Biso mean: 20.4004 Å2 / Biso min: 9.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→44.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.59→1.631 Å / Total num. of bins used: 20
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