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Open data
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Basic information
Entry | Database: PDB / ID: 4gix | ||||||
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Title | Crystal structure of human GLTP bound with 12:0 disulfatide | ||||||
![]() | Glycolipid transfer protein | ||||||
![]() | LIPID TRANSPORT / GLTP-fold | ||||||
Function / homology | ![]() glycolipid transfer activity / lipid transfer activity / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ceramide transport / Glycosphingolipid transport / glycolipid binding / intermembrane lipid transfer / response to immobilization stress / lipid binding ...glycolipid transfer activity / lipid transfer activity / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ceramide transport / Glycosphingolipid transport / glycolipid binding / intermembrane lipid transfer / response to immobilization stress / lipid binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Samygina, V.R. / Ochoa-Lizarralde, B. / Malinina, L. | ||||||
![]() | ![]() Title: Structural insights into lipid-dependent reversible dimerization of human GLTP. Authors: Samygina, V.R. / Ochoa-Lizarralde, B. / Popov, A.N. / Cabo-Bilbao, A. / Goni-de-Cerio, F. / Molotkovsky, J.G. / Patel, D.J. / Brown, R.E. / Malinina, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.1 KB | Display | ![]() |
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PDB format | ![]() | 43.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4gh0C ![]() 4ghpC ![]() 4ghsC ![]() 4gjqC ![]() 4gvtC ![]() 4gxdC ![]() 4gxgC ![]() 4h2zC ![]() 3rznS C: citing same article ( S: Starting model for refinement |
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Similar 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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 23877.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-0SG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15%PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 1, 2010 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 19652 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3RZN Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.02 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.142 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.389 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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