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Yorodumi- PDB-2ds0: Crystal structure of the earthworm lectin C-terminal domain mutan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ds0 | |||||||||
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Title | Crystal structure of the earthworm lectin C-terminal domain mutant in complex with 6'-sialyllactose | |||||||||
Components | 29-kDa galactose-binding lectin | |||||||||
Keywords | SUGAR BINDING PROTEIN / EARTHWORM LUMBRICUS TERRESTRIS / SIALIC ACID / GALACTOSE / IN VITRO EVOLUTION / BETA-TREFOIL FOLD / SUGAR COMPLEX | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Lumbricus terrestris (common earthworm) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Suzuki, R. / Fujimoto, Z. | |||||||||
Citation | Journal: J.Biochem. / Year: 2007 Title: Tailoring a novel sialic acid-binding lectin from a ricin-B chain-like galactose-binding protein by natural evolution-mimicry Authors: Yabe, R. / Suzuki, R. / Kuno, A. / Fujimoto, Z. / Jigami, Y. / Hirabayashi, J. #1: Journal: To be Published / Year: 2006 Title: Sugar complex structures of the galactose-binding lectin EW29 C-half domain from the earthworm Lumbricus terrestris Authors: Suzuki, R. / Kuno, A. / Hasegawa, T. / Hirabayashi, J. / Kasai, K. / Momma, M. / Fujimoto, Z. #2: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004 Title: Crystallization and preliminary X-ray crystallographic studies of the C-terminal domain of galactose-binding lectin EW29 from the earthworm Lubmricus terrestris Authors: Suzuki, R. / Fujimoto, Z. / Kuno, A. / Hirabayashi, J. / Kasai, K. / Hasegawa, T. #3: Journal: To be Published / Year: 2006 Title: In vitro selection of carbohydrate-binding protein by using advanced ribosome display Authors: Yabe, R. / Kuno, A. / Sawata, Y.S. / Hirabayashi, J. / Jigamai, Y. / Taira, K. / Hasegawa, T. #4: Journal: J.Biol.Chem. / Year: 1998 Title: Novel galactose-binding proteins in Annelida. Characterization of 29-kDa tandem repeat-type lectins from the earthworm Lumbricus terrestris Authors: Hirabayashi, J. / Dutta, S.K. / Kasai, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ds0.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ds0.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ds0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/2ds0 ftp://data.pdbj.org/pub/pdb/validation_reports/ds/2ds0 | HTTPS FTP |
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-Related structure data
Related structure data | 2dryC 2drzC 2d12 C: citing same article (ref.) 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: 14432.154 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN / Mutation: E148G,I227N,D230G,I231V,E237G,G239S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lumbricus terrestris (common earthworm) Plasmid: pET27 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: O96048 #2: Polysaccharide | #3: Chemical | ChemComp-SO4 / #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: 2.26 Å3/Da / Density % sol: 45.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 20% PEG8000, 0.2M sodium chloride, 0.1M phosphate-citrate, 15mg/ml 6'-sialyllactose, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 27, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 44954 / Num. obs: 22875 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 14.3 Å2 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2D12 2d12 Resolution: 1.8→22.88 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 964768.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.2003 Å2 / ksol: 0.327187 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→22.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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