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Open data
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Basic information
Entry | Database: PDB / ID: 1jzn | |||||||||
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Title | crystal structure of a galactose-specific C-type lectin | |||||||||
![]() | Galactose-specific lectin | |||||||||
![]() | SUGAR BINDING PROTEIN / C-type lectin / protein-disaccharide complex | |||||||||
Function / homology | ![]() signaling receptor activity / carbohydrate binding / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Walker, J.R. / Nagar, B. / Young, N.M. / Hirama, T. / Rini, J.M. | |||||||||
![]() | ![]() Title: X-ray Crystal Structure of a Galactose-Specific C-Type Lectin Possessing a Novel Decameric Quaternary Structure. Authors: Walker, J.R. / Nagar, B. / Young, N.M. / Hirama, T. / Rini, J.M. #1: ![]() Title: Isolation and characterization of three Ca2+-dependent beta-galactoside-specific lectins from snake venoms Authors: Gartner, T.K. / Ogilvie, M.L. #2: ![]() Title: Complete primary structure of a galactose-specific lectin from the venom of the rattlesnake Crotalus atrox. Homologies with Ca2(+)-dependent-type lectins Authors: Hirabayashi, J.T. / Kusunoki, T. / 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 | ![]() | 167.5 KB | Display | ![]() |
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PDB format | ![]() | 136 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 33.7 KB | Display | |
Data in CIF | ![]() | 49 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Details | The biological assembly is a decamer generated from the pentamer in the asymetric unit by the operation -x, y, -z + 1/2. |
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Components
-Protein / Sugars , 2 types, 10 molecules ABCDE
#1: Protein | Mass: 16312.377 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Details: Isolated from venom Source: (natural) ![]() References: UniProt: P21963 #2: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose |
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-Non-polymers , 4 types, 550 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.46 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Na acetate pH 4.6, 50 mM lactose, 40 mM CaCl2, 1.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 9, 1999 |
Radiation | Monochromator: Horizontally Focused, 3.8 degree asymmetrically cut Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8931 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→37.46 Å / Num. all: 38575 / Num. obs: 38575 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.1 Å2 / Rsym value: 0.063 |
Reflection shell | Resolution: 2.2→2.25 Å / Rsym value: 0.15 / % possible all: 80.5 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 40 Å / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS % possible obs: 79.8 % / Rmerge(I) obs: 0.156 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Positions of sulfur atoms of residue C86 in all five protein molecules were fixed during refinement as these atoms make disulfide bonds with crystallographically related molecules.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.574 Å2 / ksol: 0.358084 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→37.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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