[English] 日本語
![](img/lk-miru.gif)
- PDB-1zhz: Structure of yeast oxysterol binding protein Osh4 in complex with... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1zhz | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of yeast oxysterol binding protein Osh4 in complex with ergosterol | ||||||
![]() | KES1 protein | ||||||
![]() | LIPID BINDING PROTEIN / oxysterol / sterol binding protein | ||||||
Function / homology | ![]() Acyl chain remodelling of PS / Synthesis of bile acids and bile salts / sterol transfer activity / sterol transport / : / post-Golgi vesicle-mediated transport / ER to Golgi ceramide transport / maintenance of cell polarity / sphingolipid metabolic process / phosphatidic acid binding ...Acyl chain remodelling of PS / Synthesis of bile acids and bile salts / sterol transfer activity / sterol transport / : / post-Golgi vesicle-mediated transport / ER to Golgi ceramide transport / maintenance of cell polarity / sphingolipid metabolic process / phosphatidic acid binding / piecemeal microautophagy of the nucleus / oxysterol binding / phosphatidylinositol-4-phosphate binding / exocytosis / phosphatidylinositol-4,5-bisphosphate binding / endocytosis / Golgi membrane / lipid binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Im, Y.J. / Raychaudhuri, S. / Prinz, W.A. / Hurley, J.H. | ||||||
![]() | ![]() Title: Structural mechanism for sterol sensing and transport by OSBP-related proteins Authors: Im, Y.J. / Raychaudhuri, S. / Prinz, W.A. / Hurley, J.H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 106.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 79.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 671.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 676.5 KB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 28.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zhtC ![]() 1zhwC ![]() 1zhxSC ![]() 1zhyC ![]() 1zi7C C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 49898.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: OSH4 / Plasmid: modified pGEX4T / Species (production host): Escherichia coli / Production host: ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-ERG / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 51.8 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 29, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 39857 / Num. obs: 38934 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Biso Wilson estimate: 20.5 Å2 / Rsym value: 0.052 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Mean I/σ(I) obs: 5.2 / Num. unique all: 3883 / Rsym value: 0.283 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB Entry 1ZHX Resolution: 1.9→21.62 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 699819.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.1022 Å2 / ksol: 0.370862 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→21.62 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|