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Yorodumi- PDB-3nbe: Clitocybe nebularis ricin B-like lectin (CNL) in complex with N,N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nbe | |||||||||
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Title | Clitocybe nebularis ricin B-like lectin (CNL) in complex with N,N'-diacetyllactosediamine | |||||||||
Components | Ricin B-like lectin | |||||||||
Keywords | SUGAR BINDING PROTEIN / Clitocybe nebularis ricin B-like lectin / N / N'-diacetyllactosediamine | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Clitocybe nebularis (fungus) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | |||||||||
Authors | Renko, M. / Pohleven, J. / Sabotic, J. / Kos, J. / Turk, D. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Bivalent carbohydrate binding is required for biological activity of Clitocybe nebularis lectin (CNL), the N,N'-diacetyllactosediamine (GalNAc beta 1-4GlcNAc, LacdiNAc)-specific lectin from ...Title: Bivalent carbohydrate binding is required for biological activity of Clitocybe nebularis lectin (CNL), the N,N'-diacetyllactosediamine (GalNAc beta 1-4GlcNAc, LacdiNAc)-specific lectin from basidiomycete C. nebularis Authors: Pohleven, J. / Renko, M. / Magister, S. / Smith, D.F. / Kunzler, M. / Strukelj, B. / Turk, D. / Kos, J. / Sabotic, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nbe.cif.gz | 82.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nbe.ent.gz | 60.7 KB | Display | PDB format |
PDBx/mmJSON format | 3nbe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nbe_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3nbe_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3nbe_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 3nbe_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/3nbe ftp://data.pdbj.org/pub/pdb/validation_reports/nb/3nbe | HTTPS FTP |
-Related structure data
Related structure data | 3nbcSC 3nbdC S: Starting model for refinement C: citing same article (ref.) |
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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: 15870.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clitocybe nebularis (fungus) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2ZRS9 #2: Polysaccharide | #3: Chemical | #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: 2.56 Å3/Da / Density % sol: 51.91 % / Mosaicity: 0.999 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 0.085M HEPES sodium, 1.7%(v/v) PEG 400, 2.0M Ammonium sulfate, 19%(w/v) Glycerol, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 10, 2009 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 28570 / Num. obs: 27569 / % possible obs: 96.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.5 % / Rmerge(I) obs: 0.083 / Χ2: 2.107 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.364 / Num. unique all: 689 / Χ2: 1.081 / % possible all: 48.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NBC Resolution: 1.86→16.47 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.006 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. The structure was refined also with MAIN.
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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: 120.04 Å2 / Biso mean: 27.259 Å2 / Biso min: 9.06 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→16.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.856→1.904 Å / Total num. of bins used: 20
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