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Open data
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Basic information
Entry | Database: PDB / ID: 1is4 | |||||||||
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Title | LACTOSE-LIGANDED CONGERIN II | |||||||||
![]() | CONGERIN II | |||||||||
![]() | SUGAR BINDING PROTEIN / COMPLEX WITH LACTOSE / BETA SANDWICH | |||||||||
Function / homology | ![]() galactoside binding / laminin binding / carbohydrate binding / collagen-containing extracellular matrix / extracellular space Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Shirai, T. / Matsui, Y. / Shionyu-Mitsuyama, C. / Yamane, T. / Kamiya, H. / Ishii, C. / Ogawa, T. / Muramoto, K. | |||||||||
![]() | ![]() Title: Crystal Structure of a Conger Eel Galectin (Congerin II) at 1.45 A Resolution: Implication for the Accelerated Evolution of a New Ligand-Binding Site Following Gene Duplication Authors: Shirai, T. / Matsui, Y. / Shionyu-Mitsuyama, C. / Yamane, T. / Kamiya, H. / Ishii, C. / Ogawa, T. / Muramoto, 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 | ![]() | 42.6 KB | Display | ![]() |
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PDB format | ![]() | 28.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.5 KB | Display | ![]() |
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Full document | ![]() | 427.9 KB | Display | |
Data in XML | ![]() | 4.5 KB | Display | |
Data in CIF | ![]() | 6.7 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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Unit cell |
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Details | The second part of the biological assembly is generated by the two fold axis: y, x, -z+1. |
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Components
#1: Protein | Mass: 15354.119 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.33 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: magnesium sulfate, sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→99 Å / Num. all: 12417 / Num. obs: 12417 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.082 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 7.7 / Num. unique all: 1159 / % possible all: 92.7 |
Reflection | *PLUS Highest resolution: 1.88 Å / Lowest resolution: 99 Å / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 92.7 % / Num. unique obs: 1159 / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 7.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: CONGERIN II- LACTOSE AND MES COMPLEX Resolution: 1.9→8 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å
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Refinement | *PLUS % reflection Rfree: 4.7 % / Rfactor all: 0.17 / Rfactor obs: 0.167 / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.166 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.269 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.208 |