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- PDB-4ghp: Crystal Structure of D48V||A47D mutant of Human GLTP bound with 1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ghp | ||||||
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Title | Crystal Structure of D48V||A47D mutant of Human GLTP bound with 12:0 monosulfatide | ||||||
![]() | Glycolipid transfer protein | ||||||
![]() | LIPID TRANSPORT / GLTP-fold | ||||||
Function / homology | ![]() glycolipid transfer activity / lipid transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / Glycosphingolipid transport / glycolipid binding / intermembrane lipid transfer / response to immobilization stress ...glycolipid transfer activity / lipid transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi 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. / Popov, A.N. / 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 | ![]() | 98.1 KB | Display | ![]() |
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PDB format | ![]() | 74.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 633.8 KB | Display | ![]() |
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Full document | ![]() | 637.8 KB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gh0C ![]() 4ghsC ![]() 4gixC ![]() 4gjqC ![]() 4gvtC ![]() 4gxdC ![]() 4gxgC ![]() 4h2zC ![]() 3ricS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 23905.830 Da / Num. of mol.: 1 / Mutation: D48V, A47D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-EIS / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10-20% PEG 3350, pH 5.5-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2010 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9754 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→15 Å / Num. all: 17073 / Num. obs: 16808 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.82→1.85 Å / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3RIC Resolution: 1.9→14.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 9.308 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.183 / ESU R Free: 0.158 / 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: 49.501 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→14.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 11.1647 Å / Origin y: -0.3398 Å / Origin z: 14.492 Å
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