+
Open data
-
Basic information
Entry | Database: PDB / ID: 5ljc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of holo human CRBP1 | ||||||
![]() | Retinol-binding protein 1 | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() all-trans-retinol binding / retinoic acid biosynthetic process / vitamin A metabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zanotti, G. / Vallese, F. / Berni, R. / Menozzi, I. | ||||||
![]() | ![]() Title: Structural and molecular determinants affecting the interaction of retinol with human CRBP1. Authors: Menozzi, I. / Vallese, F. / Polverini, E. / Folli, C. / Berni, R. / Zanotti, G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 73.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 54.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5ljbSC ![]() 5ljdC ![]() 5ljeC ![]() 5ljgC ![]() 5ljhC ![]() 5ljkC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 15856.213 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Position 108 was mutated in Leu. Q108L / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-RTL / ![]() |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 40 % |
---|---|
Crystal grow![]() | Temperature: 279 K / Method: vapor diffusion / pH: 5 Details: 0.2 M ammonium chloride, 0.1 M sodium acetate, 0.2 mM zinc chloride, pH 5,0, 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.43→40.883 Å / Num. obs: 23562 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.43→1.51 Å / Redundancy: 3 % / Rmerge(I) obs: 0.504 / % possible all: 82.5 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 5LJB Resolution: 1.433→40.883 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 23.13
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.433→40.883 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|