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- PDB-3gal: CRYSTAL STRUCTURE OF HUMAN GALECTIN-7 IN COMPLEX WITH GALACTOSAMINE -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gal | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN GALECTIN-7 IN COMPLEX WITH GALACTOSAMINE | ||||||
![]() | GALECTIN-7 | ||||||
![]() | LECTIN / GALAPTIN / GALECTIN / CARBOHYDRATE BINDING | ||||||
Function / homology | ![]() heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / apoptotic process / extracellular space / extracellular exosome / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Leonidas, D.D. / Acharya, K.R. | ||||||
![]() | ![]() Title: Structural basis for the recognition of carbohydrates by human galectin-7. Authors: Leonidas, D.D. / Vatzaki, E.H. / Vorum, H. / Celis, J.E. / Madsen, P. / Acharya, K.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.4 KB | Display | ![]() |
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PDB format | ![]() | 49.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 391.4 KB | Display | ![]() |
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Full document | ![]() | 401.7 KB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 11.7 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.997677, -0.066346, -0.01544), Vector: |
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Components
#1: Protein | Mass: 14965.850 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.1 Details: CRYSTALS WERE GROWN USING THE HANGING DROP METHOD FROM DROPS CONTAINING 9 MG/ML PROTEIN AT PH 8.1 IN 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, 8.5% PEG 3350 AND ...Details: CRYSTALS WERE GROWN USING THE HANGING DROP METHOD FROM DROPS CONTAINING 9 MG/ML PROTEIN AT PH 8.1 IN 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, 8.5% PEG 3350 AND 25 MM GALACTOSAMINE. DROPS WERE EQUILIBRATED AGAINST RESERVOIRS CONTAINING 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, 17% PEG 3350 AND 50 MM GALACTOSAMINE., vapor diffusion - hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.84 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 22372 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.363 / % possible all: 98 |
Reflection | *PLUS Num. measured all: 132648 |
Reflection shell | *PLUS % possible obs: 98 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: FREE GALECTIN-7 Resolution: 1.9→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 33.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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