+
Open data
-
Basic information
Entry | Database: PDB / ID: 5yqi | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the first StARkin domain of Lam2 | ||||||
![]() | Membrane-anchored lipid-binding protein YSP2 | ||||||
![]() | TRANSPORT PROTEIN / ligand binding domain / sterol / lipid transport | ||||||
Function / homology | ![]() intracellular sterol transport / endoplasmic reticulum-plasma membrane contact site / sterol transfer activity / sterol binding / cortical endoplasmic reticulum / cholesterol transfer activity / cholesterol binding / cell periphery / mitochondrial membrane / apoptotic process ...intracellular sterol transport / endoplasmic reticulum-plasma membrane contact site / sterol transfer activity / sterol binding / cortical endoplasmic reticulum / cholesterol transfer activity / cholesterol binding / cell periphery / mitochondrial membrane / apoptotic process / endoplasmic reticulum membrane / mitochondrion / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tong, J. / Im, Y.J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural basis of sterol recognition and nonvesicular transport by lipid transfer proteins anchored at membrane contact sites Authors: Tong, J. / Manik, M.K. / Im, Y.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 50.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 33.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 420.6 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 12.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yqjSC ![]() 5yqpC ![]() 5yqqC ![]() 5yqrC ![]() 5ys0C S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 19244.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pHis2-Thr Details (production host): an N-terminal hexa-histidine tag fusion Production host: ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.54 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M MES-NaOH pH 6.0, 30% PEG3350, 0.1M KNO3 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 22632 / % possible obs: 98.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 45.5 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 1117 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5YQJ Resolution: 1.6→23.973 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.23
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→23.973 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|