[English] 日本語
![](img/lk-miru.gif)
- PDB-4kbr: Crystal structure of mouse Ceramide-1-phosphate transfer protein ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4kbr | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of mouse Ceramide-1-phosphate transfer protein (apo-form) | ||||||
![]() | Glycolipid transfer protein domain-containing protein 1 | ||||||
![]() | LIPID TRANSPORT / Lipid transfer protein / GLTP-fold / CPTP / C1P / Ceramide-1-phosphate / Protein-lipid complex / Eicosanoid | ||||||
Function / homology | ![]() Glycosphingolipid metabolism / ceramide 1-phosphate transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ceramide transport / intermembrane lipid transfer / negative regulation of NLRP3 inflammasome complex assembly / nuclear outer membrane / negative regulation of interleukin-1 beta production / negative regulation of autophagy ...Glycosphingolipid metabolism / ceramide 1-phosphate transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ceramide transport / intermembrane lipid transfer / negative regulation of NLRP3 inflammasome complex assembly / nuclear outer membrane / negative regulation of interleukin-1 beta production / negative regulation of autophagy / phospholipid binding / endosome membrane / lipid binding / Golgi apparatus / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Simanshu, D.K. / Brown, R.E. / Patel, D.J. | ||||||
![]() | ![]() Title: Non-vesicular trafficking by a ceramide-1-phosphate transfer protein regulates eicosanoids. Authors: Simanshu, D.K. / Kamlekar, R.K. / Wijesinghe, D.S. / Zou, X. / Zhai, X. / Mishra, S.K. / Molotkovsky, J.G. / Malinina, L. / Hinchcliffe, E.H. / Chalfant, C.E. / Brown, R.E. / Patel, D.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 640 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 535.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4k80C ![]() 4k84C ![]() 4k85C ![]() 4k8nC ![]() 4kbsC ![]() 4kf6C C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
-
Components
#1: Protein | Mass: 24747.330 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.3 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Bis-Tris pH 6.5, 2 M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→50 Å / Num. obs: 57653 / % possible obs: 93.5 % / Redundancy: 10 % / Rmerge(I) obs: 0.086 / Χ2: 1.091 / Net I/σ(I): 8.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: Human CPTP in complex with 2:0 C1P Resolution: 2.547→39.507 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.09 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141.47 Å2 / Biso mean: 55.3094 Å2 / Biso min: 27.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.547→39.507 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -27.1615 Å / Origin y: 27.2651 Å / Origin z: -33.5591 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|