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- PDB-3rzn: Crystal Structure of Human Glycolipid Transfer Protein complexed ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3rzn | ||||||
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Title | Crystal Structure of Human Glycolipid Transfer Protein complexed with 3-O-sulfo-galactosylceramide containing nervonoyl acyl chain (24:1) | ||||||
![]() | 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. / Cabo-Bilbao, A. / Popov, A.N. / Ochoa-Lizarralde, B. / Patel, D.J. / Brown, R.E. / Malinina, L. | ||||||
![]() | ![]() Title: Enhanced selectivity for sulfatide by engineered human glycolipid transfer protein. Authors: Samygina, V.R. / Popov, A.N. / Cabo-Bilbao, A. / Ochoa-Lizarralde, B. / Goni-de-Cerio, F. / Zhai, X. / 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 | ![]() | 118.1 KB | Display | ![]() |
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PDB format | ![]() | 90.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ricC ![]() 3rwvC ![]() 3s0iC ![]() 3s0kC ![]() 1swxS 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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Details | THE BIOLOGICAL UNIT HAS BEEN VERIFIED BY DLS METHOD. |
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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-CIS / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.47 % |
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Crystal grow | Temperature: 273 K / pH: 5.1 Details: 20-25% PEG 8000, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. obs: 96462 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.1→1.15 Å / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 3.67 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1SWX Resolution: 1.1→14.97 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.672 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.029 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→14.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.13 Å / Total num. of bins used: 20
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