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- PDB-2zqn: Crystal structure of the earthworm R-type lectin C-half in comple... -
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Basic information
Entry | Database: PDB / ID: 2zqn | ||||||||||||
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Title | Crystal structure of the earthworm R-type lectin C-half in complex with Lactose | ||||||||||||
![]() | 29-kDa galactose-binding lectin | ||||||||||||
![]() | SUGAR BINDING PROTEIN / EARTHWORM LUMBRICUS TERRESTRIS / HEMAGGLUTININ / R-TYPE LECTIN / BETA-TREFOIL FOLD / SUGAR COMPLEX / Lectin | ||||||||||||
Function / homology | ![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Suzuki, R. / Kuno, A. / Hasegawa, T. / Hirabayashi, J. / Kasai, K. / Momma, M. / Fujimoto, Z. | ||||||||||||
![]() | ![]() Title: Sugar-complex structures of the C-half domain of the galactose-binding lectin EW29 from the earthworm Lumbricus terrestris Authors: Suzuki, R. / Kuno, A. / Hasegawa, T. / Hirabayashi, J. / Kasai, K. / Momma, M. / Fujimoto, Z. #1: 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 Lumbricus terrestris Authors: Suzuki, R. / Fujimoto, Z. / Kuno, A. / Hirabayashi, J. / Kasai, K. / Hasegawa, T. #2: ![]() 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. #3: 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.7 KB | Display | ![]() |
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PDB format | ![]() | 55.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zqoC ![]() 1xyfS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 14746.550 Da / Num. of mol.: 2 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pET21 / Production host: ![]() ![]() #2: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: sodium chloride, dipotassium hydrogen phosphate, sodium dihydrogen phosphate, imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 3, 2003 |
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 27297 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2660 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1XYF Resolution: 1.9→42.29 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.764 / SU ML: 0.083 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 22.103 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→42.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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