[English] 日本語
![](img/lk-miru.gif)
- PDB-1g7y: THE CRYSTAL STRUCTURE OF THE 58KD VEGETATIVE LECTIN FROM THE TROP... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1g7y | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | THE CRYSTAL STRUCTURE OF THE 58KD VEGETATIVE LECTIN FROM THE TROPICAL LEGUME DOLICHOS BIFLORUS | |||||||||
![]() | STEM/LEAF LECTIN DB58 | |||||||||
![]() | SUGAR BINDING PROTEIN / JELLY ROLL FOLD / LECTIN | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Buts, L. / Hamelryck, T.W. / Loris, R. / Dao-Thi, M.-H. / Wyns, L. / Etzler, M.E. | |||||||||
![]() | ![]() Title: Weak protein-protein interactions in lectins: the crystal structure of a vegetative lectin from the legume Dolichos biflorus. Authors: Buts, L. / Dao-Thi, M.H. / Loris, R. / Wyns, L. / Etzler, M. / Hamelryck, T. #1: ![]() Title: Crystallisation of two related lectins from the legume plant Dolichos biflorus Authors: Dao-Thi, M. / Hamelryck, T.W. / Bouckaert, J. / Koerber, F. / Burkow, V. / Poortmans, F. / Etzler, M. / Strecker, G. / Wyns, L. / Loris, R. #2: ![]() Title: Carbohydrate binding, quaternary structure and a novel hydrophobic binding site in two legume lectins oligomers from Dolichos biflorus Authors: Hamelryck, T.W. / Loris, R. / Bouckaert, J. / Dao-Thi, M.-H. / Strecker, G. / Imberty, A. / Fernandez, E. / Wyns, L. / Etzler, M.E. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 282.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 230.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 57.8 KB | Display | |
Data in CIF | ![]() | 75.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 27146.885 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: TROPICAL LEGUME Source: (natural) ![]() Species: Vigna unguiculata / Strain: subsp. cylindrica / References: UniProt: P19588 |
---|
-Sugars , 2 types, 3 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
---|
-Non-polymers , 3 types, 53 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-MN / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.54 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 5-7 mg/ml protein; 100mM sodium citrate; 8-12%(w/v) PEG(6000); 0.2-0.4M sodium chloride, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 20, 1998 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98089 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 276382 / Num. obs: 259246 / % possible obs: 93.8 % / Observed criterion σ(I): 5 / Redundancy: 4.4 % / Biso Wilson estimate: 45.1 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 2.78 / % possible all: 95.7 |
Reflection | *PLUS Num. all: 259246 / Num. obs: 59075 / Num. measured all: 276382 |
Reflection shell | *PLUS % possible obs: 95.7 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: non-canonical legume lectin dimer (non-canonical half of a DBL tetramer) Resolution: 2.5→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2558709.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.12 Å2 / ksol: 0.289 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.8 Å2
| ||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10.1 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 38.8 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.359 / % reflection Rfree: 10 % / Rfactor Rwork: 0.314 |