[English] 日本語
![](img/lk-miru.gif)
- PDB-2dry: Crystal structure of the earthworm lectin C-terminal domain mutant -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2dry | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the earthworm lectin C-terminal domain mutant | ||||||
![]() | 29-kDa galactose-binding lectin | ||||||
![]() | SUGAR BINDING PROTEIN / EARTHWORM LUMBRICUS TERRESTRIS / SIALIC ACID / GALACTOSE / IN VITRO EVOLUTION / BETA-TREFOIL FOLD | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Suzuki, R. / Fujimoto, Z. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 71 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 51.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 460.5 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2drzC ![]() 2ds0C ![]() 2d12 C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
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.) ![]() Plasmid: pET27 / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.07 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 30% PEGMME2000, 0.2M Ammonium Sulfate, 0.1M Sodium Acetate trihydrate , pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 6, 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: 41322 / Num. obs: 21395 / % possible obs: 87.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 761.8 / Biso Wilson estimate: 19 Å2 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 82.3 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2D12 ![]() 2d12 Resolution: 1.8→22.64 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 522944.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.5549 Å2 / ksol: 0.289893 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.1 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→22.64 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
|